Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 112 of 325
Found at i:33331584 original size:13 final size:14
Alignment explanation
Indices: 33331564--33331600 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
33331554 CTACATCAAT
33331564 ATGAGCCATATCTC
1 ATGAGCCATATCTC
33331578 A-GAGCCATATCTC
1 ATGAGCCATATCTC
33331591 ATG-GCCATAT
1 ATGAGCCATAT
33331601 ACAAAATGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 20 0.91
14 2 0.09
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (14 bp):
ATGAGCCATATCTC
Found at i:33333918 original size:48 final size:48
Alignment explanation
Indices: 33333861--33333959 Score: 171
Period size: 48 Copynumber: 2.1 Consensus size: 48
33333851 CATGGATACA
* *
33333861 TAGAATACATCGTGAATCTTTTCCAATTCGGATGGCAACGCCAACCGG
1 TAGAATACATCGTGAATCTTTTCCAATTCAGATGGCAACACCAACCGG
*
33333909 TAGAATACATTGTGAATCTTTTCCAATTCAGATGGCAACACCAACCGG
1 TAGAATACATCGTGAATCTTTTCCAATTCAGATGGCAACACCAACCGG
33333957 TAG
1 TAG
33333960 GCTAATGGTC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.26
Consensus pattern (48 bp):
TAGAATACATCGTGAATCTTTTCCAATTCAGATGGCAACACCAACCGG
Found at i:33343499 original size:90 final size:90
Alignment explanation
Indices: 33343346--33343523 Score: 236
Period size: 90 Copynumber: 2.0 Consensus size: 90
33343336 ATTTGGGGTG
* * * *
33343346 ATGAGATCCCGTATAAGACCATATCTGGGATATGGCATCTGCATCGGTATGTGTTATCATGTAAG
1 ATGAGATCCCATATAAGACCATATCTGGGACATGGCATCTGCATCGCTATGTGTTACCATGTAAG
*
33343411 ACCATATC-GAGGATATGGCGTTGAT
66 ACCATATCTG-GGATATGACGTTGAT
* * *
33343436 ATGAGATCCCATGTAAGACCATGTCTGGGACATGGCAT-TGGCATCGACT-TGTGTTCCCATGTA
1 ATGAGATCCCATATAAGACCATATCTGGGACATGGCATCT-GCATCG-CTATGTGTTACCATGTA
33343499 AGACCATATCTGGGATATGACGTTG
64 AGACCATATCTGGGATATGACGTTG
33343524 GCATCTTACT
Statistics
Matches: 77, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
89 1 0.01
90 74 0.96
91 2 0.03
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (90 bp):
ATGAGATCCCATATAAGACCATATCTGGGACATGGCATCTGCATCGCTATGTGTTACCATGTAAG
ACCATATCTGGGATATGACGTTGAT
Found at i:33343860 original size:41 final size:40
Alignment explanation
Indices: 33343804--33343894 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 40
33343794 ACAAAAATTG
*
33343804 TAAAACACATAGCAATAGCGGCG-TTTTACCAAAAAACGCCAC
1 TAAAA-ACAAAGCAATAGCGGCGTTTTTA-C-AAAAACGCCAC
*
33343846 TAAAAACAAAGCAATAGCGGCGTTTTTTACAAAAACGCCGC
1 TAAAAACAAAGCAATAGCGGCG-TTTTTACAAAAACGCCAC
33343887 TAAAAACA
1 TAAAAACA
33343895 GAGAAAGCGC
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
41 34 0.76
42 6 0.13
43 5 0.11
ACGTcount: A:0.45, C:0.23, G:0.14, T:0.18
Consensus pattern (40 bp):
TAAAAACAAAGCAATAGCGGCGTTTTTACAAAAACGCCAC
Found at i:33343965 original size:41 final size:41
Alignment explanation
Indices: 33343902--33344117 Score: 369
Period size: 41 Copynumber: 5.3 Consensus size: 41
33343892 ACAGAGAAAG
33343902 CGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGAAAAA
1 CGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGAAAAA
**
33343943 CGCCGCTAAAAACCAGTTCATTAGCGGCGCTTTTGGAAAAA
1 CGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGAAAAA
*
33343984 CGCCGCTAAAAACCAGAGCATTAGCGGCGCTTGTGGAAAAA
1 CGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGAAAAA
*
33344025 CGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGCAAAA
1 CGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGAAAAA
* * *
33344066 CGCCGCTAAAAACTAGAGCATTAGTGGCGCTTTTGGCAAAA
1 CGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGAAAAA
33344107 CGCCGCTAAAA
1 CGCCGCTAAAA
33344118 GTCATATAAC
Statistics
Matches: 166, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 166 1.00
ACGTcount: A:0.33, C:0.25, G:0.24, T:0.18
Consensus pattern (41 bp):
CGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGAAAAA
Found at i:33344322 original size:67 final size:67
Alignment explanation
Indices: 33344240--33344373 Score: 259
Period size: 67 Copynumber: 2.0 Consensus size: 67
33344230 TAAAAGAGAT
*
33344240 AGTATTGAATTTAAAATATCGAATTAATTATCATTATAGTTTATGGTTTATGGTTTAAGATATAT
1 AGTATTGAATTTAAAATATCAAATTAATTATCATTATAGTTTATGGTTTATGGTTTAAGATATAT
33344305 AG
66 AG
33344307 AGTATTGAATTTAAAATATCAAATTAATTATCATTATAGTTTATGGTTTATGGTTTAAGATATAT
1 AGTATTGAATTTAAAATATCAAATTAATTATCATTATAGTTTATGGTTTATGGTTTAAGATATAT
33344372 AG
66 AG
33344374 TTTAGGGTTT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.38, C:0.03, G:0.14, T:0.45
Consensus pattern (67 bp):
AGTATTGAATTTAAAATATCAAATTAATTATCATTATAGTTTATGGTTTATGGTTTAAGATATAT
AG
Found at i:33344376 original size:21 final size:21
Alignment explanation
Indices: 33344352--33344432 Score: 81
Period size: 21 Copynumber: 3.7 Consensus size: 21
33344342 ATAGTTTATG
*
33344352 GTTTATGGTTTAAGATATATA
1 GTTTAGGGTTTAAGATATATA
* *
33344373 GTTTAGGGTTTAAGATTTTTGA
1 GTTTAGGGTTTAAGATATAT-A
* *
33344395 GTTAACTATGGTTTAAGATATATG
1 GTT---TAGGGTTTAAGATATATA
33344419 GTTTAGGGTTTAAG
1 GTTTAGGGTTTAAG
33344433 GTTTAGGAGT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
21 27 0.56
22 4 0.08
24 3 0.06
25 14 0.29
ACGTcount: A:0.28, C:0.01, G:0.25, T:0.46
Consensus pattern (21 bp):
GTTTAGGGTTTAAGATATATA
Found at i:33344423 original size:46 final size:46
Alignment explanation
Indices: 33344355--33344448 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 46
33344345 GTTTATGGTT
**
33344355 TATGGTTTAAGATATATAGTTTAGGGTTTAAGATTTTTGAGTTAAC
1 TATGGTTTAAGATATATAGTTTAGGGTTTAAGATTTAGGAGTTAAC
* *
33344401 TATGGTTTAAGATATATGGTTTAGGGTTTAAGGTTTAGGAGTTAAC
1 TATGGTTTAAGATATATAGTTTAGGGTTTAAGATTTAGGAGTTAAC
33344447 TA
1 TA
33344449 GTATTTGAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.30, C:0.02, G:0.24, T:0.44
Consensus pattern (46 bp):
TATGGTTTAAGATATATAGTTTAGGGTTTAAGATTTAGGAGTTAAC
Found at i:33345080 original size:23 final size:23
Alignment explanation
Indices: 33345019--33345081 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 23
33345009 TAATATCCTA
*
33345019 TATATGTAATTGTATTTAAATTT
1 TATATGTAATTGTATTAAAATTT
*
33345042 T-TAATTTATATT-TATTAAAATTT
1 TAT-ATGTA-ATTGTATTAAAATTT
33345065 TATATGTAATTGTATTA
1 TATATGTAATTGTATTA
33345082 GCATTTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
22 4 0.12
23 25 0.76
24 4 0.12
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (23 bp):
TATATGTAATTGTATTAAAATTT
Found at i:33350302 original size:43 final size:43
Alignment explanation
Indices: 33350255--33350400 Score: 211
Period size: 43 Copynumber: 3.4 Consensus size: 43
33350245 TTAATTTTTA
* *
33350255 TGACCTTTAGCGGCGTTTTTTGGAAAAGCGCCGCTAAAGGTCC
1 TGACCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCC
*
33350298 TGACCTTTGGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCC
1 TGACCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCC
* * * *
33350341 TGACCTTTTGCGGCGTTTGTGGGAAAAGTGCTGCTAAAGGTCA
1 TGACCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCC
* *
33350384 AGACCTTTAGCAGCGTT
1 TGACCTTTAGCGGCGTT
33350401 GTTTTCAAAT
Statistics
Matches: 93, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 93 1.00
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.27
Consensus pattern (43 bp):
TGACCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCC
Found at i:33367615 original size:21 final size:20
Alignment explanation
Indices: 33367587--33367625 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
33367577 CAAAACTTGT
*
33367587 ATAACTATTATCAAACATTC
1 ATAACTATCATCAAACATTC
*
33367607 ATAATCTATCATTAAACAT
1 ATAA-CTATCATCAAACAT
33367626 CAAAATACTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (20 bp):
ATAACTATCATCAAACATTC
Found at i:33370249 original size:16 final size:16
Alignment explanation
Indices: 33370208--33370249 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
33370198 GTAATTAAAA
33370208 ACTTAATTAATCTAATT
1 ACTT-ATTAATCTAATT
* *
33370225 AATTTTTAATCTAATT
1 ACTTATTAATCTAATT
33370241 ACTTATTAA
1 ACTTATTAA
33370250 GTTATAAGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 18 0.86
17 3 0.14
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (16 bp):
ACTTATTAATCTAATT
Found at i:33371982 original size:20 final size:20
Alignment explanation
Indices: 33371957--33371998 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
33371947 ATCCACAAAA
33371957 TCACTTTTCTCAATAAACTT
1 TCACTTTTCTCAATAAACTT
33371977 TCACTTTTCTCAATAAACTT
1 TCACTTTTCTCAATAAACTT
33371997 TC
1 TC
33371999 TTTTATCGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.45
Consensus pattern (20 bp):
TCACTTTTCTCAATAAACTT
Found at i:33373793 original size:42 final size:42
Alignment explanation
Indices: 33373678--33373795 Score: 148
Period size: 43 Copynumber: 2.8 Consensus size: 42
33373668 ATACCAATGC
**
33373678 CATATCCCAGATATGGTCTTACATGGGATCTCATATCGATGG
1 CATATCCCAGATATGGTCTTACATGAAATCTCATATCGATGG
* * *
33373720 CAATAGT-CCAGCTATGGCCTTACATGAAATCTCATATCGATGT
1 C-ATA-TCCCAGATATGGTCTTACATGAAATCTCATATCGATGG
* *
33373763 CATATCCCAGATATGGTCTTACACGTAATCTCA
1 CATATCCCAGATATGGTCTTACATGAAATCTCA
33373796 ACTAACCCTA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
41 1 0.02
42 27 0.42
43 35 0.55
44 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.31
Consensus pattern (42 bp):
CATATCCCAGATATGGTCTTACATGAAATCTCATATCGATGG
Found at i:33380764 original size:53 final size:50
Alignment explanation
Indices: 33380640--33380825 Score: 171
Period size: 49 Copynumber: 3.7 Consensus size: 50
33380630 TCTGGTACGT
*
33380640 ATAGTAGCCTACACTTAGTACTACACACATGACCTAACCATCTGATACAC
1 ATAGTAGCCTACACTTAGTACTACACACATGACCGAACCATCTGATACAC
* * * ** **
33380690 GTAGTAGCTTACACTTAGTACTACACACACGTGATCGAAGTTATC-GAGTATGC
1 ATAGTAGCCTACACTTAGTACTACACACA--TGACCGAA-CCATCTGA-TACAC
* ** *
33380743 ATAGTAGCCTACACTTAGTACTACACATGA-GACC-AATTATCTGGTACAC
1 ATAGTAGCCTACACTTAGTACTACACA-CATGACCGAACCATCTGATACAC
* * *
33380792 GTAGTAGCCTGCACTTAGTACTACACACGTGACC
1 ATAGTAGCCTACACTTAGTACTACACACATGACC
33380826 TCACAATAGA
Statistics
Matches: 110, Mismatches: 19, Indels: 15
0.76 0.13 0.10
Matches are distributed among these distances:
49 37 0.34
50 30 0.27
51 3 0.03
52 8 0.07
53 31 0.28
54 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (50 bp):
ATAGTAGCCTACACTTAGTACTACACACATGACCGAACCATCTGATACAC
Found at i:33381102 original size:27 final size:27
Alignment explanation
Indices: 33381072--33381125 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
33381062 TCATACAACC
* *
33381072 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
33381099 CATGTAACAATAATTTGCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
33381126 TCACATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:33382166 original size:17 final size:17
Alignment explanation
Indices: 33382144--33382180 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
33382134 TTAAGTACCC
33382144 AAATGTCAAAATTTTCG
1 AAATGTCAAAATTTTCG
*
33382161 AAATGTCAAAATTTTTG
1 AAATGTCAAAATTTTCG
33382178 AAA
1 AAA
33382181 GAAATTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.08, G:0.11, T:0.35
Consensus pattern (17 bp):
AAATGTCAAAATTTTCG
Found at i:33384430 original size:41 final size:42
Alignment explanation
Indices: 33384312--33384430 Score: 141
Period size: 43 Copynumber: 2.8 Consensus size: 42
33384302 TACATAGTAC
* * **
33384312 CATACCAATGCCATATCCCAGATATGGTCTTACATGGGATCT
1 CATATCAATGCCATATCCCAGATATGGTCTTACACGAAATCT
* * * *
33384354 CATATCGATGCTAATAGCCCAGATATGGTCGTACACGAAATCT
1 CATATCAATGC-CATATCCCAGATATGGTCTTACACGAAATCT
*
33384397 CATATCAATGCCATATCCCA-AGATGGTCTTACAC
1 CATATCAATGCCATATCCCAGATATGGTCTTACAC
33384431 ATAATTTCAA
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
41 12 0.19
42 16 0.25
43 35 0.56
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (42 bp):
CATATCAATGCCATATCCCAGATATGGTCTTACACGAAATCT
Found at i:33385319 original size:39 final size:40
Alignment explanation
Indices: 33385252--33385329 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 40
33385242 ACCAAATAAC
*
33385252 TAAAATGCCCTTTTTGCCAAACTTTAAAATTTTTTCTCAA
1 TAAAATGCCCTTTTTGCCAAACTGTAAAATTTTTTCTCAA
33385292 TAAAATGCCC-TTTTGCCAAACTGTAAAATTTTTTCTCA
1 TAAAATGCCCTTTTTGCCAAACTGTAAAATTTTTTCTCA
33385330 CCATGTCCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 27 0.73
40 10 0.27
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.41
Consensus pattern (40 bp):
TAAAATGCCCTTTTTGCCAAACTGTAAAATTTTTTCTCAA
Found at i:33397432 original size:27 final size:27
Alignment explanation
Indices: 33397401--33397454 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
33397391 TATTCAACTC
*
33397401 ATACGCCAAATAAGCTTCATAACCCTT
1 ATACGCCAAATAAGCTTAATAACCCTT
33397428 ATACGCCAAATAAGCTTAATAACCCTT
1 ATACGCCAAATAAGCTTAATAACCCTT
33397455 TCTCAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.39, C:0.28, G:0.07, T:0.26
Consensus pattern (27 bp):
ATACGCCAAATAAGCTTAATAACCCTT
Found at i:33407613 original size:2 final size:2
Alignment explanation
Indices: 33407606--33407634 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
33407596 GTTTCAAATT
33407606 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
33407635 GCTTCCTTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33411013 original size:8 final size:8
Alignment explanation
Indices: 33411000--33411026 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
33410990 ACTTCGTATG
33411000 TACATATA
1 TACATATA
33411008 TACATATA
1 TACATATA
33411016 TACATATA
1 TACATATA
33411024 TAC
1 TAC
33411027 TACTTAAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (8 bp):
TACATATA
Found at i:33413000 original size:21 final size:21
Alignment explanation
Indices: 33412976--33413021 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
33412966 AACTACTCCA
33412976 TGCATAATTTTAGCTTTTGAT
1 TGCATAATTTTAGCTTTTGAT
33412997 TGCATAATTTTAGCTTTTGAT
1 TGCATAATTTTAGCTTTTGAT
33413018 TGCA
1 TGCA
33413022 AAAAGAACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.11, G:0.15, T:0.50
Consensus pattern (21 bp):
TGCATAATTTTAGCTTTTGAT
Found at i:33413065 original size:2 final size:2
Alignment explanation
Indices: 33413058--33413088 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
33413048 TTGAGAAGCT
33413058 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
33413089 CAAATAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33413795 original size:23 final size:22
Alignment explanation
Indices: 33413768--33413830 Score: 58
Period size: 22 Copynumber: 2.8 Consensus size: 22
33413758 ATATTTAATT
33413768 ATTTTTTAAAATTTTTAAAAATA
1 ATTTTTTAAAATTTTTAAAAA-A
*
33413791 A--TTTTAATAATTTTTTAAAAA
1 ATTTTTTAA-AATTTTTAAAAAA
* *
33413812 ATATTTTTATATTTTTTAA
1 AT-TTTTTAAAATTTTTAA
33413831 TTTTAAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
21 8 0.25
22 11 0.34
23 8 0.25
24 5 0.16
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTTTTAAAATTTTTAAAAAA
Found at i:33413802 original size:22 final size:22
Alignment explanation
Indices: 33413771--33413830 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 22
33413761 TTTAATTATT
33413771 TTTTAA-AATTTTT-AAAAATAA
1 TTTTAATAATTTTTAAAAAAT-A
33413792 TTTTAATAATTTTTTAAAAAATA
1 TTTTAATAA-TTTTTAAAAAATA
* *
33413815 TTTTTATATTTTTTAA
1 TTTTAATAATTTTTAA
33413831 TTTTAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 6 0.18
22 9 0.26
23 13 0.38
24 6 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTAATAATTTTTAAAAAATA
Found at i:33425164 original size:36 final size:36
Alignment explanation
Indices: 33425117--33425188 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
33425107 AGAATAATCA
33425117 ATTTGTTATTTGACCTAATATACAAGGATTAATTTG
1 ATTTGTTATTTGACCTAATATACAAGGATTAATTTG
33425153 ATTTGTTATTTGACCTAATATACAAGGATTAATTTG
1 ATTTGTTATTTGACCTAATATACAAGGATTAATTTG
33425189 TTCTTTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.44
Consensus pattern (36 bp):
ATTTGTTATTTGACCTAATATACAAGGATTAATTTG
Found at i:33430277 original size:24 final size:25
Alignment explanation
Indices: 33430233--33430294 Score: 117
Period size: 24 Copynumber: 2.5 Consensus size: 25
33430223 TCACTACCTG
33430233 ATCAGGATGCTCGCAAGAACTATAC
1 ATCAGGATGCTCGCAAGAACTATAC
33430258 ATCAGGATGCT-GCAAGAACTATAC
1 ATCAGGATGCTCGCAAGAACTATAC
33430282 ATCAGGATGCTCG
1 ATCAGGATGCTCG
33430295 AGAGGGATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
24 24 0.67
25 12 0.33
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.21
Consensus pattern (25 bp):
ATCAGGATGCTCGCAAGAACTATAC
Found at i:33436300 original size:40 final size:40
Alignment explanation
Indices: 33436255--33436421 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
33436245 CGGAATATAA
33436255 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
33436295 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
33436335 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
33436375 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
33436414 CCGGATAT
1 CCGGATAT
33436422 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:33444307 original size:40 final size:40
Alignment explanation
Indices: 33444262--33444428 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
33444252 CGGAATATAA
33444262 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
33444302 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
33444342 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
33444382 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
33444421 CCGGATAT
1 CCGGATAT
33444429 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:33450446 original size:29 final size:29
Alignment explanation
Indices: 33450380--33450519 Score: 196
Period size: 29 Copynumber: 4.9 Consensus size: 29
33450370 AAACTCACAT
* *
33450380 ACCTATATCTGGCCCATTAAGCCC-AATC
1 ACCTATATATGGCCCATTAGGCCCAAATC
33450408 A--TATTCATATGGCCCATTAGGCCCAAATC
1 ACCTA-T-ATATGGCCCATTAGGCCCAAATC
33450437 ACCTATATATGGCCCATTAGGCCCAAATC
1 ACCTATATATGGCCCATTAGGCCCAAATC
33450466 ACCTATATATGGCCCATTAGGCCCAAATC
1 ACCTATATATGGCCCATTAGGCCCAAATC
* * *
33450495 ACATTTATATGGCCCGTTAGGCCCA
1 ACCTATATATGGCCCATTAGGCCCA
33450520 GTCACATTCA
Statistics
Matches: 102, Mismatches: 5, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
26 2 0.02
27 1 0.01
28 17 0.17
29 79 0.77
30 1 0.01
31 2 0.02
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.26
Consensus pattern (29 bp):
ACCTATATATGGCCCATTAGGCCCAAATC
Found at i:33450768 original size:16 final size:16
Alignment explanation
Indices: 33450747--33450783 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
33450737 AAACTTTCGG
33450747 CTTTTCGACATTTTGA
1 CTTTTCGACATTTTGA
* *
33450763 CTTTTCGGCATTTTGG
1 CTTTTCGACATTTTGA
33450779 CTTTT
1 CTTTT
33450784 GCCGATTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.19, G:0.16, T:0.54
Consensus pattern (16 bp):
CTTTTCGACATTTTGA
Found at i:33454788 original size:28 final size:29
Alignment explanation
Indices: 33454756--33454857 Score: 118
Period size: 29 Copynumber: 3.6 Consensus size: 29
33454746 TACCTGTATC
*
33454756 TGGCCCATTAAGCCC-AATCATATTTATA
1 TGGCCCATTAGGCCCAAATCATATTTATA
*
33454784 TGGCCCATTAGGCCCAAATCACT-TATATA
1 TGGCCCATTAGGCCCAAATCA-TATTTATA
* * *
33454813 TGACTCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCATATTTATA
* *
33454842 TGGCCCGTTAGACCCA
1 TGGCCCATTAGGCCCA
33454858 GTCACTTTCA
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
28 14 0.23
29 46 0.75
30 1 0.02
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.28
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCATATTTATA
Found at i:33454813 original size:29 final size:28
Alignment explanation
Indices: 33454756--33454870 Score: 117
Period size: 29 Copynumber: 4.0 Consensus size: 28
33454746 TACCTGTATC
* *
33454756 TGGCCCATTAAGCCC-AATCATATTTATA
1 TGGCCCATTAGGCCCAAATCA-CTTTATA
33454784 TGGCCCATTAGGCCCAAATCACTTATATA
1 TGGCCCATTAGGCCCAAATCACTT-TATA
* *
33454813 TGACTCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCAC-TTTATA
* * *
33454842 TGGCCCGTTAGACCC-AGTCACTTTCATA
1 TGGCCCATTAGGCCCAAATCACTTT-ATA
33454870 T
1 T
33454871 TCATGCTCAC
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
27 3 0.04
28 25 0.34
29 44 0.59
30 2 0.03
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (28 bp):
TGGCCCATTAGGCCCAAATCACTTTATA
Found at i:33456232 original size:16 final size:16
Alignment explanation
Indices: 33456208--33456239 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
33456198 AAGTTCGGGA
33456208 TTTCAGGATTTTTGGG
1 TTTCAGGATTTTTGGG
*
33456224 TTTCGGGATTTTTGGG
1 TTTCAGGATTTTTGGG
33456240 GCGTTACAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.09, C:0.06, G:0.34, T:0.50
Consensus pattern (16 bp):
TTTCAGGATTTTTGGG
Found at i:33456282 original size:6 final size:6
Alignment explanation
Indices: 33456271--33456324 Score: 63
Period size: 6 Copynumber: 9.0 Consensus size: 6
33456261 AAATAAGAAC
* * * *
33456271 AATAAA AATAAA GAGAAA GATAAA AATAAA AATAAA AATAAA CATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
*
33456319 GATAAA
1 AATAAA
33456325 TGGACTTAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (6 bp):
AATAAA
Found at i:33456323 original size:18 final size:18
Alignment explanation
Indices: 33456271--33456324 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
33456261 AAATAAGAAC
*
33456271 AATAAAAATAAAGAGAAA
1 AATAAAAATAAAGATAAA
* *
33456289 GATAAAAATAAAAATAAA
1 AATAAAAATAAAGATAAA
*
33456307 AATAAACATAAAGATAAA
1 AATAAAAATAAAGATAAA
33456325 TGGACTTAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (18 bp):
AATAAAAATAAAGATAAA
Found at i:33458728 original size:47 final size:47
Alignment explanation
Indices: 33458661--33458783 Score: 237
Period size: 47 Copynumber: 2.6 Consensus size: 47
33458651 GATGCGAGCG
33458661 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
*
33458708 TCCGAACTCGTTGAGTTGAGTCCAAGTTCGTGAGATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
33458755 TCCGAACTCGTTGAGTTGAGTCCGAGTTC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC
33458784 ACTTATGGAT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 74 1.00
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.28
Consensus pattern (47 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
Found at i:33462855 original size:40 final size:40
Alignment explanation
Indices: 33462811--33462918 Score: 132
Period size: 40 Copynumber: 2.7 Consensus size: 40
33462801 GAAATTATAA
* *
33462811 CCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC-AT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCGAGT--CATACTAT
*
33462851 CCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTCATTCTAT
1 CCGGGCTAAGACCCGAAGGCAATT-GTGCGAGTCATACTAT
*
33462891 CCGGGCTAAGACCCGAAGGCATTTGTGC
1 CCGGGCTAAGACCCGAAGGCAATTGTGC
33462919 AAATCGTGAT
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
38 1 0.02
39 5 0.08
40 52 0.87
41 2 0.03
ACGTcount: A:0.23, C:0.26, G:0.30, T:0.21
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCGAGTCATACTAT
Found at i:33471030 original size:40 final size:39
Alignment explanation
Indices: 33470865--33471048 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
33470855 AAATTGAATG
* * *
33470865 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
33470905 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
33470945 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
33470985 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
33471024 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
33471049 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:33471073 original size:80 final size:81
Alignment explanation
Indices: 33470905--33471093 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
33470895 GCTGGAAATT
* * * *
33470905 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
33470970 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
33470986 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
33471049 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
33471065 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
33471094 AACGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:33473262 original size:15 final size:15
Alignment explanation
Indices: 33473223--33473302 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
33473213 GTATCTTGGG
*
33473223 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
33473238 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
* *
33473253 TTTCTTTATTCCGGG
1 TTTCTTTATTCTGGA
*
33473268 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
33473283 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
33473297 TTTCTT
1 TTTCTT
33473303 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
14 10 0.19
15 41 0.77
16 2 0.04
ACGTcount: A:0.10, C:0.19, G:0.14, T:0.57
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:33473292 original size:30 final size:30
Alignment explanation
Indices: 33473214--33473301 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
33473204 CATAGTATCG
* * *
33473214 TATCTTGGGTTTCTTTA-TCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCC-GGATTTCTC
*
33473244 TAT-TCTGGATTTCTTTATTCCGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCCGGATTTCTC
*
33473274 TATCTTGGATTTCTTTATT-CGGTTTTCT
1 TATCTTGGATTTCTTTATTCCGGATTTCT
33473302 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
29 9 0.18
30 37 0.74
31 4 0.08
ACGTcount: A:0.10, C:0.18, G:0.16, T:0.56
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCCGGATTTCTC
Found at i:33491456 original size:40 final size:40
Alignment explanation
Indices: 33491401--33491650 Score: 376
Period size: 40 Copynumber: 6.2 Consensus size: 40
33491391 AACATTGGAA
33491401 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
33491441 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
33491481 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
33491521 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * ** *
33491561 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGC-AAATC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
33491600 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
33491641 CTATATCCGG
1 ATATATCCGG
33491651 TTAAATCCCG
Statistics
Matches: 189, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 3 0.02
40 185 0.98
41 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:33500627 original size:12 final size:12
Alignment explanation
Indices: 33500610--33500642 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
33500600 GGACCCGTCC
33500610 ATATTAATTTTT
1 ATATTAATTTTT
33500622 ATATT-ATTTTT
1 ATATTAATTTTT
33500633 ATA-TAATTTT
1 ATATTAATTTT
33500643 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:33511106 original size:14 final size:16
Alignment explanation
Indices: 33511087--33511125 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
33511077 AAGAAAATGA
*
33511087 TGATATATGACA-A-G
1 TGATATATGAAATATG
33511101 TGATATATGAAATATG
1 TGATATATGAAATATG
33511117 TGATATATG
1 TGATATATG
33511126 TTATGTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.50
15 1 0.05
16 10 0.45
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.36
Consensus pattern (16 bp):
TGATATATGAAATATG
Found at i:33512658 original size:39 final size:39
Alignment explanation
Indices: 33512612--33512771 Score: 266
Period size: 39 Copynumber: 4.1 Consensus size: 39
33512602 AAGCAAGACA
33512612 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
* *
33512651 TTGGAAATGTATCCGGGCTAAAGAGCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
*
33512690 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
* * *
33512729 CTGGAAATGTATCCGAGCTAAAGTCCCGCAGGCTTTGTG
1 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
33512768 CTGG
1 CTGG
33512772 TAATATAATT
Statistics
Matches: 114, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 114 1.00
ACGTcount: A:0.22, C:0.24, G:0.31, T:0.23
Consensus pattern (39 bp):
CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
Found at i:33517814 original size:39 final size:39
Alignment explanation
Indices: 33517760--33517916 Score: 233
Period size: 39 Copynumber: 4.0 Consensus size: 39
33517750 CAAGACATTA
*
33517760 GAAATGTACCCGGGCTAAAGACCCGCAGGCTTCGTGCTG
1 GAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTGCTG
33517799 GAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTGCTG
1 GAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTGCTG
* * *
33517838 GAAATGTATCCGGGCTAAAGTCCCACAGGCTTCGTGCTA
1 GAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTGCTG
* * * * *
33517877 GAAATGTATCTGAGTTAAAGTCCCGCAGGCTTTGTGCTG
1 GAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTGCTG
33517916 G
1 G
33517917 TAATATAATT
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 108 1.00
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.23
Consensus pattern (39 bp):
GAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTGCTG
Found at i:33519536 original size:51 final size:50
Alignment explanation
Indices: 33519408--33519546 Score: 183
Period size: 49 Copynumber: 2.8 Consensus size: 50
33519398 TATTGTGAGG
* * * * * * *
33519408 TCACGTGTTTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGGA
33519458 TGCA--TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGTGA
1 T-CACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTG-GA
33519508 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACC
33519547 AGATAGCTTC
Statistics
Matches: 78, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
49 39 0.50
50 3 0.04
51 36 0.46
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (50 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGGA
Found at i:33529030 original size:30 final size:30
Alignment explanation
Indices: 33528994--33529053 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
33528984 ACAAGTTTGG
33528994 TGTTTAGAGAAAACCTATCGTGAAAACAAA
1 TGTTTAGAGAAAACCTATCGTGAAAACAAA
33529024 TGTTTAGAGAAAACCTATCGTGAAAACAAA
1 TGTTTAGAGAAAACCTATCGTGAAAACAAA
33529054 CTTGGGAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.47, C:0.13, G:0.17, T:0.23
Consensus pattern (30 bp):
TGTTTAGAGAAAACCTATCGTGAAAACAAA
Found at i:33529208 original size:30 final size:30
Alignment explanation
Indices: 33529172--33529231 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
33529162 AGCACTCTAG
*
33529172 AGTTAAAATTCCCAAAATACTCCTAAAACT
1 AGTTAAAATTCCCAAAATACCCCTAAAACT
* *
33529202 AGTTAAAATTTCTAAAATACCCCTAAAACT
1 AGTTAAAATTCCCAAAATACCCCTAAAACT
33529232 CATAGGCCCT
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:0.47, C:0.22, G:0.03, T:0.28
Consensus pattern (30 bp):
AGTTAAAATTCCCAAAATACCCCTAAAACT
Found at i:33530739 original size:45 final size:45
Alignment explanation
Indices: 33530683--33530773 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
33530673 GAATTATGTA
*
33530683 ATCTGAACTCATTGAGTTGTGGTCTGAGTTCATGATATATGTGAC
1 ATCTGAACTCATTAAGTTGTGGTCTGAGTTCATGATATATGTGAC
**
33530728 ATCTGAACTCATTAAGTTGTGGTCTGAGTTTGTGATATATGTGAC
1 ATCTGAACTCATTAAGTTGTGGTCTGAGTTCATGATATATGTGAC
33530773 A
1 A
33530774 CATGTTTTGG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.38
Consensus pattern (45 bp):
ATCTGAACTCATTAAGTTGTGGTCTGAGTTCATGATATATGTGAC
Found at i:33532164 original size:42 final size:43
Alignment explanation
Indices: 33532097--33532205 Score: 141
Period size: 43 Copynumber: 2.6 Consensus size: 43
33532087 GATTTGAGAT
* * *
33532097 TTACGTGTACGACCATGTCTAGGAC-ATCGACATC-ATATTTGA
1 TTACATGTAAGACCATGTCTGGGACAAT-GACATCGATATTTGA
* * *
33532139 TTTCATGTAAGACCCTGTCTGGGACAATGGCATCGATATTTGA
1 TTACATGTAAGACCATGTCTGGGACAATGACATCGATATTTGA
33532182 TTACATGTAAGACCATGTCTGGGA
1 TTACATGTAAGACCATGTCTGGGA
33532206 TGTTGGCATT
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
42 25 0.44
43 32 0.56
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (43 bp):
TTACATGTAAGACCATGTCTGGGACAATGACATCGATATTTGA
Found at i:33538908 original size:16 final size:16
Alignment explanation
Indices: 33538887--33538940 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
33538877 TCGGCAGATC
33538887 CCGAAAAGCTGAAATG
1 CCGAAAAGCTGAAATG
33538903 CCGAAAAG-TCGAAATG
1 CCGAAAAGCT-GAAATG
* * *
33538919 CTGAAATGCTGAAAAG
1 CCGAAAAGCTGAAATG
33538935 CCGAAA
1 CCGAAA
33538941 GTTTGGCTAC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 1 0.03
16 30 0.94
17 1 0.03
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (16 bp):
CCGAAAAGCTGAAATG
Found at i:33538921 original size:24 final size:24
Alignment explanation
Indices: 33538887--33538940 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
33538877 TCGGCAGATC
33538887 CCGAAAAGCTGAAATGCCGAAAAG
1 CCGAAAAGCTGAAATGCCGAAAAG
* * *
33538911 TCGAAATGCTGAAATGCTGAAAAG
1 CCGAAAAGCTGAAATGCCGAAAAG
33538935 CCGAAA
1 CCGAAA
33538941 GTTTGGCTAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (24 bp):
CCGAAAAGCTGAAATGCCGAAAAG
Found at i:33539225 original size:28 final size:28
Alignment explanation
Indices: 33539154--33539267 Score: 115
Period size: 28 Copynumber: 4.1 Consensus size: 28
33539144 AGCATAATTG
* **
33539154 TAAATGTGATTGGGCCTAAT-GGCCGTA
1 TAAATGAGATTGGGCCTAATGGGCCACA
* *
33539181 TTAATGTGATTTGGGCCTAATGGGCCACA
1 TAAATGAGA-TTGGGCCTAATGGGCCACA
* * *
33539210 TAAATGAGATTAGGCCTAATGAGCCATA
1 TAAATGAGATTGGGCCTAATGGGCCACA
*
33539238 TGAAA-GAGATTGGGCCTAATGGGCTACA
1 T-AAATGAGATTGGGCCTAATGGGCCACA
33539266 TA
1 TA
33539268 TAGGTATGTG
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
27 9 0.12
28 48 0.67
29 15 0.21
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (28 bp):
TAAATGAGATTGGGCCTAATGGGCCACA
Found at i:33539251 original size:56 final size:56
Alignment explanation
Indices: 33539154--33539267 Score: 149
Period size: 56 Copynumber: 2.0 Consensus size: 56
33539144 AGCATAATTG
* * * * * *
33539154 TAAATGTGATTGGGCCTAATGGCCGTATTAATGTGATTTGGGCCTAATGGGCCACA
1 TAAATGAGATTAGGCCTAATGGCCATATGAAAGAGATTTGGGCCTAATGGGCCACA
*
33539210 TAAATGAGATTAGGCCTAATGAGCCATATGAAAGAGA-TTGGGCCTAATGGGCTACA
1 TAAATGAGATTAGGCCTAATG-GCCATATGAAAGAGATTTGGGCCTAATGGGCCACA
33539266 TA
1 TA
33539268 TAGGTATGTG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
56 39 0.78
57 11 0.22
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (56 bp):
TAAATGAGATTAGGCCTAATGGCCATATGAAAGAGATTTGGGCCTAATGGGCCACA
Found at i:33540293 original size:18 final size:19
Alignment explanation
Indices: 33540262--33540298 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
33540252 AGTTAGTAAT
33540262 AAAGAAATGGGAAA-AAAA
1 AAAGAAATGGGAAAGAAAA
33540280 AAAGAAA-GGAGAAAGAAAA
1 AAAGAAATGG-GAAAGAAAA
33540299 TGATGAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 2 0.12
18 11 0.65
19 4 0.24
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.03
Consensus pattern (19 bp):
AAAGAAATGGGAAAGAAAA
Found at i:33541728 original size:40 final size:40
Alignment explanation
Indices: 33541620--33541748 Score: 201
Period size: 40 Copynumber: 3.3 Consensus size: 40
33541610 ACTAAGATCT
*
33541620 GAAGCCATTTGTGCGAGTTACTAAATCCGGGCTAAG-CCC
1 GAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCC
*
33541659 GAAGGCA-TTGTGCGAGTTACTAAATCCGGGTTAAGTCCC
1 GAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCC
*
33541698 GAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCC
1 GAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGTCCC
33541738 GAAGGCATTTG
1 GAAGGCATTTG
33541749 AACGAGTAGC
Statistics
Matches: 83, Mismatches: 4, Indels: 5
0.90 0.04 0.05
Matches are distributed among these distances:
38 27 0.33
39 16 0.19
40 38 0.46
41 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
GAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCC
Found at i:33545893 original size:43 final size:43
Alignment explanation
Indices: 33545725--33545894 Score: 143
Period size: 43 Copynumber: 4.0 Consensus size: 43
33545715 TAGGATTTCT
* * *
33545725 GATATGTGATTTCGTGTAAGA-CACGTCTGGGACGATGGCATC
1 GATATTTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATC
* * * *
33545767 GAT-TTGAGATTTATGTGTAAGACCATGTCTGGGAC-TTCGACATC
1 GATATT-TGA-TTACGTGTAAGACCACGTCTGGGACGTT-GGCATC
* * ** * *
33545811 G-TATTTGATTTCGTCTAAGACCTTGTCTAGGATAG-TGGCATC
1 GATATTTGATTACGTGTAAGACCACGTCTGGGA-CGTTGGCATC
*
33545853 GATATTTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 GATATTTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
33545895 TTTACGAGCT
Statistics
Matches: 97, Mismatches: 22, Indels: 17
0.71 0.16 0.12
Matches are distributed among these distances:
41 1 0.01
42 31 0.32
43 46 0.47
44 19 0.20
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.33
Consensus pattern (43 bp):
GATATTTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATC
Found at i:33547151 original size:29 final size:29
Alignment explanation
Indices: 33547109--33547167 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
33547099 ACGGGCTAGA
*
33547109 CACACGGGCGTGTCTAATTCCATGTGAGG
1 CACACGGGCGTGTCTAATGCCATGTGAGG
*
33547138 CACACGGGCTTGTCTAATGCCATGTGAGG
1 CACACGGGCGTGTCTAATGCCATGTGAGG
33547167 C
1 C
33547168 GCACAGCCTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.20, C:0.25, G:0.31, T:0.24
Consensus pattern (29 bp):
CACACGGGCGTGTCTAATGCCATGTGAGG
Found at i:33550780 original size:16 final size:16
Alignment explanation
Indices: 33550759--33550791 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
33550749 CGACAAATCT
*
33550759 CGAAATGTCGAAAAGC
1 CGAAATGCCGAAAAGC
33550775 CGAAATGCCGAAAAGC
1 CGAAATGCCGAAAAGC
33550791 C
1 C
33550792 AGAAGTTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.24, G:0.24, T:0.09
Consensus pattern (16 bp):
CGAAATGCCGAAAAGC
Found at i:33551077 original size:29 final size:28
Alignment explanation
Indices: 33551008--33551105 Score: 92
Period size: 28 Copynumber: 3.5 Consensus size: 28
33550998 ATTGCATGAC
* * * *
33551008 TATGAATGTGATTAGGGCTGATGAGCTA
1 TATGAATGTGATTTGGGCTAATGGGCCA
33551036 TATGAATGTGATTTGGGCATAATGGGCCA
1 TATGAATGTGATTTGGGC-TAATGGGCCA
* * *
33551065 TATGAATGAGA-TTGGGCCTAGTAGGCCA
1 TATGAATGTGATTTGGG-CTAATGGGCCA
*
33551093 TATGCATGT-ATTT
1 TATGAATGTGATTT
33551106 AGACTGATGA
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
27 1 0.02
28 39 0.67
29 18 0.31
ACGTcount: A:0.28, C:0.10, G:0.30, T:0.33
Consensus pattern (28 bp):
TATGAATGTGATTTGGGCTAATGGGCCA
Found at i:33555897 original size:40 final size:40
Alignment explanation
Indices: 33555853--33556020 Score: 246
Period size: 40 Copynumber: 4.2 Consensus size: 40
33555843 CTCTGTGCTA
* *
33555853 AGTTACTAAATTCGCACTAAGATCCGAAGGCAATTGTGCG
1 AGTTACTAAATCCGGACTAAGATCCGAAGGCAATTGTGCG
* ** *
33555893 AGTTACTAAACCCAAACTAAGATCCGAAGGCATTTGTGCG
1 AGTTACTAAATCCGGACTAAGATCCGAAGGCAATTGTGCG
* *
33555933 AGTTACTAAATCCGGACTAAGATCCGAAGACATTTGTGCG
1 AGTTACTAAATCCGGACTAAGATCCGAAGGCAATTGTGCG
*
33555973 AGTTACTAAATCCGGACTAAGATCTGAAGGCAATTGTGCG
1 AGTTACTAAATCCGGACTAAGATCCGAAGGCAATTGTGCG
*
33556013 AGCTACTA
1 AGTTACTA
33556021 TAACCGGGCC
Statistics
Matches: 115, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 115 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.24
Consensus pattern (40 bp):
AGTTACTAAATCCGGACTAAGATCCGAAGGCAATTGTGCG
Found at i:33556055 original size:80 final size:80
Alignment explanation
Indices: 33555856--33556055 Score: 188
Period size: 80 Copynumber: 2.5 Consensus size: 80
33555846 TGTGCTAAGT
* * * * * **
33555856 TACTAAATTCGCACTAAGATCCGAAGGCAATTGTGCGAGTTACTAAACCCAAACTAAGATCCGAA
1 TACTAAATCCGGACCAAGATCCGAAGACATTTGAACGAGTTACTAAACCCAAACTAAGATCCGAA
* *
33555921 GGCATTTGTGCGAGT
66 GGCAATTGTGCGAGC
* ** * ** *
33555936 TACTAAATCCGGACTAAGATCCGAAGACATTTGTGCGAGTTACTAAATCCGGACTAAGATCTGAA
1 TACTAAATCCGGACCAAGATCCGAAGACATTTGAACGAGTTACTAAACCCAAACTAAGATCCGAA
33556001 GGCAATTGTGCGAGC
66 GGCAATTGTGCGAGC
* * **
33556016 TACTATAA-CCGGGCCATG-TCCCGAAGGTATTTGAACGAGT
1 TACTA-AATCCGGACCAAGAT-CCGAAGACATTTGAACGAGT
33556056 GGCTATATCT
Statistics
Matches: 101, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
79 1 0.01
80 98 0.97
81 2 0.02
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (80 bp):
TACTAAATCCGGACCAAGATCCGAAGACATTTGAACGAGTTACTAAACCCAAACTAAGATCCGAA
GGCAATTGTGCGAGC
Found at i:33557994 original size:27 final size:27
Alignment explanation
Indices: 33557964--33558065 Score: 125
Period size: 27 Copynumber: 3.7 Consensus size: 27
33557954 CTGCTAGAAT
* *
33557964 AGATATTGTGACAGAGTCACCAGATAC
1 AGATATTGTGGCAGAGCCACCAGATAC
* *
33557991 AGATATTGTGGCAGAGCCAGCAGAAAC
1 AGATATTGTGGCAGAGCCACCAGATAC
*
33558018 AGATATTTGTGGTAGAGCCACCAGAT-C
1 AGATA-TTGTGGCAGAGCCACCAGATAC
*
33558045 AGATATTTGTGGCAAAGCCAC
1 AGATA-TTGTGGCAGAGCCAC
33558066 TAGAACGTTT
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
27 48 0.74
28 17 0.26
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22
Consensus pattern (27 bp):
AGATATTGTGGCAGAGCCACCAGATAC
Found at i:33561681 original size:28 final size:27
Alignment explanation
Indices: 33561602--33561681 Score: 97
Period size: 27 Copynumber: 2.9 Consensus size: 27
33561592 CTGCCAGAAT
* * *
33561602 AGATATTGTGACAGAGTCACCAGATAC
1 AGATATTGTGGCAGAGCCACCAGAAAC
***
33561629 AGATATTGTGGCAGAGCCTGTAGAAAC
1 AGATATTGTGGCAGAGCCACCAGAAAC
33561656 AGATATTTGTGGCAGAGCCACCAGAA
1 AGATA-TTGTGGCAGAGCCACCAGAA
33561682 TCCTTCCTCC
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
27 26 0.60
28 17 0.40
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.21
Consensus pattern (27 bp):
AGATATTGTGGCAGAGCCACCAGAAAC
Found at i:33565493 original size:28 final size:29
Alignment explanation
Indices: 33565453--33565517 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 29
33565443 ATTGCATGAC
* *
33565453 TATGAATGTGATTAGGGC-CGATGGGCCA
1 TATGAATGTGATTAGGGCACAATAGGCCA
* *
33565481 TATGAATGTGATTTGGGCATAATAGGCCA
1 TATGAATGTGATTAGGGCACAATAGGCCA
33565510 TATGAATG
1 TATGAATG
33565518 AGATGGGCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 17 0.53
29 15 0.47
ACGTcount: A:0.29, C:0.11, G:0.31, T:0.29
Consensus pattern (29 bp):
TATGAATGTGATTAGGGCACAATAGGCCA
Found at i:33565535 original size:27 final size:28
Alignment explanation
Indices: 33565473--33565540 Score: 84
Period size: 27 Copynumber: 2.4 Consensus size: 28
33565463 ATTAGGGCCG
*
33565473 ATGGGCCATATGAATGTGATTTGGGCATA
1 ATGGGCCATATGAATGAGA-TTGGGCATA
* *
33565502 ATAGGCCATATGAATGAGA-TGGGCTTA
1 ATGGGCCATATGAATGAGATTGGGCATA
*
33565529 GTGGGCCATATG
1 ATGGGCCATATG
33565541 CATGTATGTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 17 0.50
29 17 0.50
ACGTcount: A:0.28, C:0.12, G:0.32, T:0.28
Consensus pattern (28 bp):
ATGGGCCATATGAATGAGATTGGGCATA
Found at i:33566792 original size:17 final size:18
Alignment explanation
Indices: 33566759--33566792 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
33566749 TTGAAAGAAG
33566759 GGTTTTCAATGAAAACAA
1 GGTTTTCAATGAAAACAA
*
33566777 GGTTTTCGAT-AAAACA
1 GGTTTTCAATGAAAACA
33566793 CTTCAATGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (18 bp):
GGTTTTCAATGAAAACAA
Found at i:33578021 original size:40 final size:40
Alignment explanation
Indices: 33577971--33578075 Score: 124
Period size: 40 Copynumber: 2.6 Consensus size: 40
33577961 CGACTGCTCG
* * *
33577971 ATTGTCTTCGGGACATAGCCCGG-TTATAGTGATTCGCACA
1 ATTGCCTTCGGGACATAGCCCGGATT-TAGTAACTCGCACA
33578011 ATTGCCTTCGGGA-ATTAGCCCGGATTTAGTAACTCGCACA
1 ATTGCCTTCGGGACA-TAGCCCGGATTTAGTAACTCGCACA
** *
33578051 AAAGCCTTCGGGACTTAGCCCGGAT
1 ATTGCCTTCGGGACATAGCCCGGAT
33578076 ACCATTCGAA
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
39 1 0.02
40 53 0.95
41 2 0.04
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.27
Consensus pattern (40 bp):
ATTGCCTTCGGGACATAGCCCGGATTTAGTAACTCGCACA
Found at i:33578797 original size:40 final size:40
Alignment explanation
Indices: 33578735--33578922 Score: 279
Period size: 40 Copynumber: 4.7 Consensus size: 40
33578725 CCAGCATGAT
*
33578735 TGCTCTTCGGGACCTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * *
33578775 TGCTCCTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * * *
33578815 TGCTCTTCGGAACTTAGTCCGGATACGTCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
33578855 TGCTCTTCGGGACTTAGCCCGAATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
33578895 TGCTCTTCGGGACTTAGCCCGGAT-CATC
1 TGCTCTTCGGGACTTAGCCCGGATACATC
33578923 GTCGAGACCT
Statistics
Matches: 133, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
39 3 0.02
40 130 0.98
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:33578839 original size:80 final size:80
Alignment explanation
Indices: 33578709--33578922 Score: 286
Period size: 80 Copynumber: 2.7 Consensus size: 80
33578699 AGGCACGGAG
* * * *
33578709 GCCCGAATACACGTCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATACATCACTAGCACGA
1 GCCCGAATACA--TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGA
33578774 ATGCTCCTCGGAACTTA
64 ATGCTCCTCGGAACTTA
* * * * * *
33578791 GTCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACGTCACTAGCATGAAT
1 GCCCGAATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAAT
* *
33578856 GCTCTTCGGGACTTA
66 GCTCCTCGGAACTTA
*
33578871 GCCCGAATATATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT-CATC
1 GCCCGAATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATC
33578923 GTCGAGACCT
Statistics
Matches: 114, Mismatches: 18, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
79 3 0.03
80 102 0.89
82 9 0.08
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.23
Consensus pattern (80 bp):
GCCCGAATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAAT
GCTCCTCGGAACTTA
Found at i:33578878 original size:23 final size:23
Alignment explanation
Indices: 33578852--33578915 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 23
33578842 TCACTAGCAT
33578852 GAATGCTCTTCGGGACTTAGCCC
1 GAATGCTCTTCGGGACTTAGCCC
* * *
33578875 GAAT-AT-ATC---AC-TAGCAC
1 GAATGCTCTTCGGGACTTAGCCC
33578892 GAATGCTCTTCGGGACTTAGCCC
1 GAATGCTCTTCGGGACTTAGCCC
33578915 G
1 G
33578916 GATCATCGTC
Statistics
Matches: 29, Mismatches: 6, Indels: 12
0.62 0.13 0.26
Matches are distributed among these distances:
17 9 0.31
18 3 0.10
19 2 0.07
21 2 0.07
22 3 0.10
23 10 0.34
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.25
Consensus pattern (23 bp):
GAATGCTCTTCGGGACTTAGCCC
Found at i:33581553 original size:47 final size:47
Alignment explanation
Indices: 33581478--33581588 Score: 152
Period size: 47 Copynumber: 2.4 Consensus size: 47
33581468 CCCCTCGGGA
* * *
33581478 CTTATCACATT-TATACACTTTCATATTCATCGCATTGGCCATTCGGC
1 CTTATCAC-TTATATACACTTTCACATTCATCACATCGGCCATTCGGC
* *
33581525 CTTATCACTTATATACACTTTGACATTCATCACATCGGTCATTCGGC
1 CTTATCACTTATATACACTTTCACATTCATCACATCGGCCATTCGGC
*
33581572 CTTATCACATATATACA
1 CTTATCACTTATATACA
33581589 TCTCATACAT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
46 2 0.04
47 55 0.96
ACGTcount: A:0.27, C:0.27, G:0.09, T:0.37
Consensus pattern (47 bp):
CTTATCACTTATATACACTTTCACATTCATCACATCGGCCATTCGGC
Found at i:33581650 original size:46 final size:46
Alignment explanation
Indices: 33581592--33581727 Score: 254
Period size: 46 Copynumber: 3.0 Consensus size: 46
33581582 ATATACATCT
* *
33581592 CATACATGTTTCATACTAGCCATTTGGCTTTACCACACATATATCA
1 CATACATATTTCACACTAGCCATTTGGCTTTACCACACATATATCA
33581638 CATACATATTTCACACTAGCCATTTGGCTTTACCACACATATATCA
1 CATACATATTTCACACTAGCCATTTGGCTTTACCACACATATATCA
33581684 CATACATATTTCACACTAGCCATTTGGCTTTACCACACATATAT
1 CATACATATTTCACACTAGCCATTTGGCTTTACCACACATATAT
33581728 ATATTTAACT
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 88 1.00
ACGTcount: A:0.32, C:0.27, G:0.07, T:0.34
Consensus pattern (46 bp):
CATACATATTTCACACTAGCCATTTGGCTTTACCACACATATATCA
Found at i:33584080 original size:45 final size:45
Alignment explanation
Indices: 33584010--33584096 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
33584000 TATGTAATCT
*
33584010 GAACTCATTGAGTTGTAGTCTGAGTTCATGATATACGTGACATCC
1 GAACTCATTGAGTTGTAGTCCGAGTTCATGATATACGTGACATCC
* * * *
33584055 GAACTCGTTGAGTTGTGGTCCGAGTTCGTGATATATGTGACA
1 GAACTCATTGAGTTGTAGTCCGAGTTCATGATATACGTGACA
33584097 CATGCTTTGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.33
Consensus pattern (45 bp):
GAACTCATTGAGTTGTAGTCCGAGTTCATGATATACGTGACATCC
Found at i:33589857 original size:39 final size:39
Alignment explanation
Indices: 33589745--33589938 Score: 244
Period size: 39 Copynumber: 4.9 Consensus size: 39
33589735 TCGTTCAAAC
* * ** * *
33589745 GCCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAAT
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATT
* *
33589785 GCCTTCGGGACTTAACCCGGATATCACAACTCGCACAATT
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATT
* *
33589825 GCCTTCGGGCTTAGCCCGGATATCATAGCTCGCACCATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
* *
33589864 GCCTTCGGGCTTAGCCCGGATATCATAATTCGCACATTT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
* *
33589903 GCCTTCGGGCTTAGCCCGGATATCACAATTCGCACA
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACA
33589939 TTCATACACA
Statistics
Matches: 137, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 96 0.70
40 41 0.30
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24
Consensus pattern (39 bp):
GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
Found at i:33592300 original size:43 final size:43
Alignment explanation
Indices: 33592244--33592407 Score: 163
Period size: 43 Copynumber: 3.8 Consensus size: 43
33592234 AGCTCGTACA
* * *
33592244 ATGCC-ATATCCCAGATATGGTCTTACATGTTATCACATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCACATATCG
* * * * *
33592286 ATGCCACTGTCCCAGGCAAGGTCTTACATGAAATCGA-ATAACG
1 ATGCCAATGTCCCAGACATGGTCTTACATGTAATC-ACATATCG
* * ** *
33592329 ATGCCAATGTCTCAAACATGGTCTTACACATAATCACA-ATACA
1 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCACATAT-CG
*
33592372 ATTCCAATGTCCCAGACATGGTCTTACATGTAATCA
1 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCA
33592408 TATCTCGGTA
Statistics
Matches: 95, Mismatches: 23, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
42 7 0.07
43 87 0.92
44 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACATGTAATCACATATCG
Found at i:33596323 original size:40 final size:40
Alignment explanation
Indices: 33596264--33596481 Score: 354
Period size: 40 Copynumber: 5.5 Consensus size: 40
33596254 AACCCAAGTA
* *
33596264 CCTTC-GGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
33596302 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
33596342 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
33596382 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAACTG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
33596422 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCAC-CATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
33596461 CCTTCGGGACTTAGCCCGGAT
1 CCTTCGGGACTTAGCCCGGAT
33596482 GTCATCCGAA
Statistics
Matches: 170, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
38 5 0.03
39 30 0.18
40 134 0.79
41 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:33601322 original size:21 final size:21
Alignment explanation
Indices: 33601287--33601327 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
33601277 CCTCTACCCG
*
33601287 TCAACTCTTGCAACTGAGCTT
1 TCAACTCTTGCAACTCAGCTT
**
33601308 TCAACTCTTTTAACTCAGCT
1 TCAACTCTTGCAACTCAGCT
33601328 GGTGCCATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.29, G:0.10, T:0.37
Consensus pattern (21 bp):
TCAACTCTTGCAACTCAGCTT
Found at i:33605540 original size:40 final size:40
Alignment explanation
Indices: 33605490--33605574 Score: 152
Period size: 40 Copynumber: 2.1 Consensus size: 40
33605480 TATAACCACA
*
33605490 TGCACGAATGCCTTCGGGTCTTAGCCCCGATAGAACGACT
1 TGCACAAATGCCTTCGGGTCTTAGCCCCGATAGAACGACT
*
33605530 TGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAACGACT
1 TGCACAAATGCCTTCGGGTCTTAGCCCCGATAGAACGACT
33605570 TGCAC
1 TGCAC
33605575 GTATTAGCCC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.24, C:0.29, G:0.25, T:0.22
Consensus pattern (40 bp):
TGCACAAATGCCTTCGGGTCTTAGCCCCGATAGAACGACT
Found at i:33605598 original size:28 final size:28
Alignment explanation
Indices: 33605550--33605603 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
33605540 CCTTCGGGTC
*
33605550 TTAGCCCGGATAGAACGACTTGCACGTA
1 TTAGCCCGGATAGAACAACTTGCACGTA
**
33605578 TTAGCCCGGATTTAACAACTTGCACG
1 TTAGCCCGGATAGAACAACTTGCACG
33605604 AATGCCTTCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (28 bp):
TTAGCCCGGATAGAACAACTTGCACGTA
Found at i:33605650 original size:40 final size:40
Alignment explanation
Indices: 33605578--33605710 Score: 142
Period size: 40 Copynumber: 3.3 Consensus size: 40
33605568 CTTGCACGTA
* * *
33605578 TTAGCCCGGATTTAA-CAACTTGCACGAATGCCTTCGGGTC
1 TTAGCCCGGATATAATC-ACTAGCACAAATGCCTTCGGGTC
* * * *
33605618 TTAGCCCGGATGTAGTCGCTAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
* * * * *
33605658 TTAACCCGGATATAATTACTAGCATAAATGTCTTCGGGAC
1 TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
33605698 TTAGCCCGGATAT
1 TTAGCCCGGATAT
33605711 CATTCAATTG
Statistics
Matches: 76, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
40 75 0.99
41 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.29
Consensus pattern (40 bp):
TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
Found at i:33605666 original size:108 final size:108
Alignment explanation
Indices: 33605475--33605669 Score: 286
Period size: 108 Copynumber: 1.8 Consensus size: 108
33605465 CGGAATACAA
* *
33605475 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCCGATAGAACGACTTGCACAAATG
1 CCGGATATAACAACATGCACGAATGCCTTCGGGTCTTAGCCCCGATAGAACGACTAGCACAAATG
*
33605540 CCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACGTATTAGC
66 CCTTCGGGTCTTAACCCGGATAGAACGACTTGCACGTATTAGC
* * * * *
33605583 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT-GTAGTCG-CTAGCACAAT
1 CCGGATATAACAACATGCACGAATGCCTTCGGGTCTTAGCCCCGATAG-A-ACGACTAGCACAAA
33605646 TGCCTTCGGGTCTTAACCCGGATA
64 TGCCTTCGGGTCTTAACCCGGATA
33605670 TAATTACTAG
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
107 1 0.01
108 74 0.96
109 2 0.03
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (108 bp):
CCGGATATAACAACATGCACGAATGCCTTCGGGTCTTAGCCCCGATAGAACGACTAGCACAAATG
CCTTCGGGTCTTAACCCGGATAGAACGACTTGCACGTATTAGC
Found at i:33608089 original size:40 final size:40
Alignment explanation
Indices: 33608015--33608233 Score: 354
Period size: 40 Copynumber: 5.5 Consensus size: 40
33608005 AACCCAAGTA
* *
33608015 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
*
33608054 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATC
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
33608094 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
33608134 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAACTG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
33608174 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCAC-CATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
33608213 CCTTCGGGACTTAGCCCGGAT
1 CCTTCGGGACTTAGCCCGGAT
33608234 GTCATCCGAA
Statistics
Matches: 169, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
39 36 0.21
40 132 0.78
41 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:33614866 original size:40 final size:39
Alignment explanation
Indices: 33614821--33614950 Score: 136
Period size: 40 Copynumber: 3.3 Consensus size: 39
33614811 CGGAATATAA
33614821 CCGGATATAACCATGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAT-TGCACAAATGCCTTCGGGTCTTAGC
* * * *
33614861 CCGGATAGAATGTC-TCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAA--CCATTGCACAAATGCCTTCGGGTCTTAGC
* * * * *
33614901 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCA-TTGCACAAATGCCTTCGGGTCTTAGC
33614941 CCGGATATAA
1 CCGGATATAA
33614951 TTTCCAGCAT
Statistics
Matches: 72, Mismatches: 14, Indels: 8
0.77 0.15 0.09
Matches are distributed among these distances:
38 1 0.01
40 69 0.96
41 1 0.01
42 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25
Consensus pattern (39 bp):
CCGGATATAACCATTGCACAAATGCCTTCGGGTCTTAGC
Found at i:33614965 original size:40 final size:40
Alignment explanation
Indices: 33614837--33614988 Score: 148
Period size: 40 Copynumber: 3.8 Consensus size: 40
33614827 ATAACCATGT
* * *
33614837 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTC-
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTC-CA
* ** * *
33614877 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
33614917 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
33614957 GCATAATTGTCTTCGGGAT-TTAGCCCGGATAT
1 GCACAATTGCCTTCGGG-TCTTAGCCCGGATAT
33614989 CATTCAATTT
Statistics
Matches: 91, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
39 2 0.02
40 86 0.95
41 3 0.03
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
Found at i:33614971 original size:80 final size:80
Alignment explanation
Indices: 33614837--33614986 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 80
33614827 ATAACCATGT
*
33614837 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTCGCACGAATGCCTTCGGG-TCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGAT-TTAGC
33614901 CCGGATGTAGCCACTA
65 CCGGATGTAGCCACTA
* * * * *
33614917 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGATTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTC-GCACGAA-TGCCTTCGGGATTTAG
33614980 CCCGGAT
64 CCCGGAT
33614987 ATCATTCAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
79 3 0.05
80 57 0.93
81 1 0.02
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGATTTAGCC
CGGATGTAGCCACTA
Found at i:33624145 original size:40 final size:39
Alignment explanation
Indices: 33624100--33624229 Score: 136
Period size: 40 Copynumber: 3.3 Consensus size: 39
33624090 CGGAATATAA
33624100 CCGGATATAACCATGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAT-TGCACAAATGCCTTCGGGTCTTAGC
* * * *
33624140 CCGGATAGAATGTC-TCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAA--CCATTGCACAAATGCCTTCGGGTCTTAGC
* * * * *
33624180 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCA-TTGCACAAATGCCTTCGGGTCTTAGC
33624220 CCGGATATAA
1 CCGGATATAA
33624230 TTTCCAGCAT
Statistics
Matches: 72, Mismatches: 14, Indels: 8
0.77 0.15 0.09
Matches are distributed among these distances:
38 1 0.01
40 69 0.96
41 1 0.01
42 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25
Consensus pattern (39 bp):
CCGGATATAACCATTGCACAAATGCCTTCGGGTCTTAGC
Found at i:33624244 original size:40 final size:40
Alignment explanation
Indices: 33624116--33624267 Score: 148
Period size: 40 Copynumber: 3.8 Consensus size: 40
33624106 ATAACCATGT
* * *
33624116 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTC-
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTC-CA
* ** * *
33624156 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
33624196 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
33624236 GCATAATTGTCTTCGGGAT-TTAGCCCGGATAT
1 GCACAATTGCCTTCGGG-TCTTAGCCCGGATAT
33624268 CATTCAATTT
Statistics
Matches: 91, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
39 2 0.02
40 86 0.95
41 3 0.03
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
Found at i:33624250 original size:80 final size:80
Alignment explanation
Indices: 33624116--33624265 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 80
33624106 ATAACCATGT
*
33624116 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTCGCACGAATGCCTTCGGG-TCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGAT-TTAGC
33624180 CCGGATGTAGCCACTA
65 CCGGATGTAGCCACTA
* * * * *
33624196 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGATTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTC-GCACGAA-TGCCTTCGGGATTTAG
33624259 CCCGGAT
64 CCCGGAT
33624266 ATCATTCAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
79 3 0.05
80 57 0.93
81 1 0.02
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGATTTAGCC
CGGATGTAGCCACTA
Found at i:33627872 original size:43 final size:43
Alignment explanation
Indices: 33627825--33627939 Score: 135
Period size: 43 Copynumber: 2.7 Consensus size: 43
33627815 TCACATATCA
* * *
33627825 ATGCCACTGTCCCAGGCAAGGTCTTACATGAAATCGAATAACG
1 ATGCCAATGTCCCAGACAAGGTCTTACACGAAATCGAATAACG
* * *
33627868 ATGCCAATGTCCCAGACATGGTCTTATACGTAATCGAATAACG
1 ATGCCAATGTCCCAGACAAGGTCTTACACGAAATCGAATAACG
*
33627911 ATG-TAGATGTCCCAGA-AATGGTCTTACAC
1 ATGCCA-ATGTCCCAGACAA-GGTCTTACAC
33627940 ATAATCACAA
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
42 2 0.03
43 59 0.97
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.24
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACAAGGTCTTACACGAAATCGAATAACG
Found at i:33634315 original size:10 final size:10
Alignment explanation
Indices: 33634275--33634317 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
33634265 CATCATCATC
*
33634275 AAAAATTTTT
1 AAAAATTATT
*
33634285 AAATATTATT
1 AAAAATTATT
33634295 -AAAATTA-T
1 AAAAATTATT
33634303 AAAAATTATT
1 AAAAATTATT
33634313 AAAAA
1 AAAAA
33634318 AAATTAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
8 1 0.04
9 13 0.46
10 14 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
AAAAATTATT
Found at i:33640158 original size:12 final size:11
Alignment explanation
Indices: 33640139--33640168 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
33640129 TTCCTAATTC
33640139 TTTTTTTCTTT
1 TTTTTTTCTTT
33640150 TTCTTTTTCTTT
1 TT-TTTTTCTTT
33640162 TTTTTTT
1 TTTTTTT
33640169 GAAAAAACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:33641777 original size:10 final size:11
Alignment explanation
Indices: 33641755--33641804 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
33641745 TGTTTAAACC
*
33641755 TATTTTTTTAA
1 TATTTTTATAA
33641766 TATTTTTA-AA
1 TATTTTTATAA
*
33641776 TAATTTTAATAA
1 T-ATTTTTATAA
*
33641788 TTTTTTTATAA
1 TATTTTTATAA
33641799 TATTTT
1 TATTTT
33641805 ACTAACAAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
10 3 0.09
11 26 0.81
12 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TATTTTTATAA
Found at i:33642292 original size:19 final size:20
Alignment explanation
Indices: 33642256--33642293 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
33642246 TGATGTATAC
*
33642256 TTTATGTTGATATCACATTA
1 TTTATGTTGATATAACATTA
33642276 TTTATGTT-ATATAACATT
1 TTTATGTTGATATAACATT
33642294 TTCATAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.53
Consensus pattern (20 bp):
TTTATGTTGATATAACATTA
Found at i:33642332 original size:21 final size:22
Alignment explanation
Indices: 33642291--33642337 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 22
33642281 GTTATATAAC
*
33642291 ATTT-TCATAAATAATTT-AAA
1 ATTTATCAAAAATAATTTAAAA
33642311 ATTTATCAAAAAT-ATTTAAAAA
1 ATTTATCAAAAATAATTT-AAAA
33642333 ATTTA
1 ATTTA
33642338 AAATTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 8 0.35
21 7 0.30
22 8 0.35
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTTATCAAAAATAATTTAAAA
Found at i:33643800 original size:19 final size:19
Alignment explanation
Indices: 33643776--33643814 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
33643766 CAACTGTAAG
33643776 ATAACTTATGATTTCATCA
1 ATAACTTATGATTTCATCA
33643795 ATAACTTATGATTTCATCA
1 ATAACTTATGATTTCATCA
33643814 A
1 A
33643815 CGTTCTACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.41
Consensus pattern (19 bp):
ATAACTTATGATTTCATCA
Found at i:33646165 original size:27 final size:29
Alignment explanation
Indices: 33646102--33646163 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
33646092 TTATCATTAT
*
33646102 CTTATAATGATTAAAAAAAGAGAGTCACC
1 CTTATAATGATTAAAAAAAGAGAGCCACC
33646131 CTTATAATGATTAAAAAAAGAGAGCCACC
1 CTTATAATGATTAAAAAAAGAGAGCCACC
33646160 CTTA
1 CTTA
33646164 ATATTCTTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.24
Consensus pattern (29 bp):
CTTATAATGATTAAAAAAAGAGAGCCACC
Found at i:33647889 original size:31 final size:31
Alignment explanation
Indices: 33647854--33647916 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
33647844 AGAGTAAAAG
33647854 CAACTAACTCTAAGTTTATTAATTAAATTTT
1 CAACTAACTCTAAGTTTATTAATTAAATTTT
*
33647885 CAACTAACTCTAGGTTTATTAATTAAATTTT
1 CAACTAACTCTAAGTTTATTAATTAAATTTT
33647916 C
1 C
33647917 TTTCTAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.37, C:0.14, G:0.05, T:0.44
Consensus pattern (31 bp):
CAACTAACTCTAAGTTTATTAATTAAATTTT
Found at i:33649502 original size:27 final size:28
Alignment explanation
Indices: 33649470--33649701 Score: 309
Period size: 27 Copynumber: 8.6 Consensus size: 28
33649460 AAGTACTCCC
*
33649470 GATTTACAGAATTACCGTTTTACCCTCA
1 GATTTACAGAATTACTGTTTTACCCTCA
*
33649498 G-TTTATAGAATTACTGTTTTACCCTC-
1 GATTTACAGAATTACTGTTTTACCCTCA
** * *
33649524 GATTTGTAAAATTACCGTTTTACCCTC-
1 GATTTACAGAATTACTGTTTTACCCTCA
*
33649551 GATTTACAGAATTACCGTTTTACCCTCA
1 GATTTACAGAATTACTGTTTTACCCTCA
*
33649579 G-TTTACAGAATTACTATTTTACCCTC-
1 GATTTACAGAATTACTGTTTTACCCTCA
33649605 GATTTACAGAATTACTGTTTTACCCTCA
1 GATTTACAGAATTACTGTTTTACCCTCA
* *
33649633 G-TTTACAGAATTATTGTTTTACCCT-T
1 GATTTACAGAATTACTGTTTTACCCTCA
33649659 GATTTACAGAATTACTGTTTTACCCTC-
1 GATTTACAGAATTACTGTTTTACCCTCA
*
33649686 GATTTACAAAATTACT
1 GATTTACAGAATTACT
33649702 AAAATACCCT
Statistics
Matches: 183, Mismatches: 15, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
26 3 0.02
27 177 0.97
28 3 0.02
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (28 bp):
GATTTACAGAATTACTGTTTTACCCTCA
Found at i:33649709 original size:27 final size:27
Alignment explanation
Indices: 33649652--33649711 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
33649642 ATTATTGTTT
* * ****
33649652 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTAAAA
33649679 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTCGATTTACAAAATTACTAAAA
33649706 TACCCT
1 TACCCT
33649712 TGGTTTGTGA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACTAAAA
Found at i:33649711 original size:81 final size:81
Alignment explanation
Indices: 33649469--33649701 Score: 353
Period size: 81 Copynumber: 2.9 Consensus size: 81
33649459 AAAGTACTCC
* **
33649469 CGATTTACAGAATTACCGTTTTACCCTCAGTTTATAGAATTACTGTTTTACCCTCGATTTGTAAA
1 CGATTTACAGAATTACCGTTTTACCCTCAGTTTACAGAATTACTGTTTTACCCTCGATTTACAAA
*
33649534 ATTACCGTTTTACCCT
66 ATTACTGTTTTACCCT
* *
33649550 CGATTTACAGAATTACCGTTTTACCCTCAGTTTACAGAATTACTATTTTACCCTCGATTTACAGA
1 CGATTTACAGAATTACCGTTTTACCCTCAGTTTACAGAATTACTGTTTTACCCTCGATTTACAAA
33649615 ATTACTGTTTTACCCT
66 ATTACTGTTTTACCCT
** *
33649631 C-AGTTTACAGAATTATTGTTTTACCCT-TGATTTACAGAATTACTGTTTTACCCTCGATTTACA
1 CGA-TTTACAGAATTACCGTTTTACCCTCAG-TTTACAGAATTACTGTTTTACCCTCGATTTACA
33649694 AAATTACT
64 AAATTACT
33649702 AAAATACCCT
Statistics
Matches: 139, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
80 2 0.01
81 137 0.99
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.41
Consensus pattern (81 bp):
CGATTTACAGAATTACCGTTTTACCCTCAGTTTACAGAATTACTGTTTTACCCTCGATTTACAAA
ATTACTGTTTTACCCT
Found at i:33650968 original size:25 final size:25
Alignment explanation
Indices: 33650939--33650986 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
33650929 TTATAATATG
* * *
33650939 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
33650964 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
33650987 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:33651074 original size:20 final size:20
Alignment explanation
Indices: 33651029--33651087 Score: 93
Period size: 20 Copynumber: 3.0 Consensus size: 20
33651019 ATAAATATGG
33651029 TATGTATGATATGCACAT-A
1 TATGTATGATATGCACATGA
* *
33651048 AATGTATGCTATGCACATGA
1 TATGTATGATATGCACATGA
33651068 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
33651088 GGTAATCATA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
19 16 0.46
20 19 0.54
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.34
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:33651165 original size:24 final size:24
Alignment explanation
Indices: 33651138--33651304 Score: 257
Period size: 24 Copynumber: 7.0 Consensus size: 24
33651128 GAGGAAGTGA
33651138 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
33651162 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
33651186 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
33651210 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
33651233 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
33651257 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
33651281 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
33651305 ATGATAAAGC
Statistics
Matches: 135, Mismatches: 5, Indels: 5
0.93 0.03 0.03
Matches are distributed among these distances:
23 23 0.17
24 101 0.75
25 11 0.08
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:33651255 original size:71 final size:71
Alignment explanation
Indices: 33651138--33651305 Score: 257
Period size: 71 Copynumber: 2.3 Consensus size: 71
33651128 GAGGAAGTGA
33651138 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCC
33651203 AGTTATC
65 AGTTATC
** *
33651210 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCA
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCA
*
33651275 GTTATT
66 GTTATC
*
33651281 AAAAGAGGC-TAGGCCTCCAGTTATA
1 AAAAG-GGCTTATGCC-CCAGTTATA
33651306 TGATAAAGCA
Statistics
Matches: 89, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
71 54 0.61
72 35 0.39
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (71 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCA
GTTATC
Found at i:33651569 original size:30 final size:31
Alignment explanation
Indices: 33651496--33651589 Score: 172
Period size: 31 Copynumber: 3.1 Consensus size: 31
33651486 CGTTTACAGT
33651496 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
33651527 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
33651558 AAAGG-TTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
33651588 AA
1 AA
33651590 TATGAAAAGG
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
30 26 0.42
31 36 0.58
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:33654454 original size:27 final size:27
Alignment explanation
Indices: 33654416--33654648 Score: 319
Period size: 27 Copynumber: 8.6 Consensus size: 27
33654406 CCAGTACTCC
*
33654416 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
*
33654443 C-AGTTTATAGAATTACTGTTTTACCCT
1 CGA-TTTACAGAATTACTGTTTTACCCT
** * *
33654470 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
*
33654497 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
*
33654524 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACTGTTTTACCCT
33654551 CGATTTACAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
*
33654578 C-AGTTTACAGAATTATTGTTTTACCCT
1 CGA-TTTACAGAATTACTGTTTTACCCT
*
33654605 TGATTTACAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
*
33654632 CGATTTACAAAATTACT
1 CGATTTACAGAATTACT
33654649 AAAATACCCT
Statistics
Matches: 184, Mismatches: 16, Indels: 12
0.87 0.08 0.06
Matches are distributed among these distances:
26 3 0.02
27 178 0.97
28 3 0.02
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.41
Consensus pattern (27 bp):
CGATTTACAGAATTACTGTTTTACCCT
Found at i:33654656 original size:27 final size:27
Alignment explanation
Indices: 33654599--33654658 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
33654589 ATTATTGTTT
* * ****
33654599 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTAAAA
33654626 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTCGATTTACAAAATTACTAAAA
33654653 TACCCT
1 TACCCT
33654659 TGGTTTGTGA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACTAAAA
Found at i:33654658 original size:81 final size:81
Alignment explanation
Indices: 33654416--33654648 Score: 353
Period size: 81 Copynumber: 2.9 Consensus size: 81
33654406 CCAGTACTCC
* **
33654416 CGATTTACAGAATTACCGTTTTACCCTCAGTTTATAGAATTACTGTTTTACCCTCGATTTGTAAA
1 CGATTTACAGAATTACCGTTTTACCCTCAGTTTACAGAATTACTGTTTTACCCTCGATTTACAAA
*
33654481 ATTACCGTTTTACCCT
66 ATTACTGTTTTACCCT
* *
33654497 CGATTTACAGAATTACCGTTTTACCCTCAGTTTACAGAATTACTATTTTACCCTCGATTTACAGA
1 CGATTTACAGAATTACCGTTTTACCCTCAGTTTACAGAATTACTGTTTTACCCTCGATTTACAAA
33654562 ATTACTGTTTTACCCT
66 ATTACTGTTTTACCCT
** *
33654578 C-AGTTTACAGAATTATTGTTTTACCCT-TGATTTACAGAATTACTGTTTTACCCTCGATTTACA
1 CGA-TTTACAGAATTACCGTTTTACCCTCAG-TTTACAGAATTACTGTTTTACCCTCGATTTACA
33654641 AAATTACT
64 AAATTACT
33654649 AAAATACCCT
Statistics
Matches: 139, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
80 2 0.01
81 137 0.99
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.41
Consensus pattern (81 bp):
CGATTTACAGAATTACCGTTTTACCCTCAGTTTACAGAATTACTGTTTTACCCTCGATTTACAAA
ATTACTGTTTTACCCT
Found at i:33655915 original size:25 final size:25
Alignment explanation
Indices: 33655886--33655933 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
33655876 TTATAATATG
* * *
33655886 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
33655911 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
33655934 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:33656002 original size:20 final size:20
Alignment explanation
Indices: 33655977--33656035 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
33655967 TAAATATGGT
33655977 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
* *
33655997 ATGTATGCTATGCACATGAT
1 ATGTATGATATGCACATGAA
33656017 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
33656036 GGTAATCATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:33656113 original size:24 final size:24
Alignment explanation
Indices: 33656086--33656238 Score: 254
Period size: 24 Copynumber: 6.4 Consensus size: 24
33656076 GAGGAAGTGA
33656086 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
33656110 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
33656134 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
33656158 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
33656181 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
33656205 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
33656229 AAAAGAGGCT
1 AAAAG-GGCT
33656239 AGGCCTCTAG
Statistics
Matches: 124, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
23 23 0.19
24 97 0.78
25 4 0.03
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:33656479 original size:31 final size:31
Alignment explanation
Indices: 33656444--33656538 Score: 181
Period size: 31 Copynumber: 3.1 Consensus size: 31
33656434 CGTTTACAGT
33656444 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
33656475 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
33656506 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
33656537 AA
1 AA
33656539 TATGAAAAGG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:33659198 original size:20 final size:21
Alignment explanation
Indices: 33659162--33659208 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
33659152 AAATAATTAA
* *
33659162 ATATAA-TACTATTTATAAAT
1 ATATAATTACTATATATAAAC
*
33659182 ATATAATTA-TATATATACAC
1 ATATAATTACTATATATAAAC
33659202 ATATAAT
1 ATATAAT
33659209 AGAAACATAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (21 bp):
ATATAATTACTATATATAAAC
Found at i:33659384 original size:33 final size:33
Alignment explanation
Indices: 33659347--33659417 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
33659337 ATACATTAAT
33659347 AATAAT-ATATGCTAATAACAATAATAATATATA
1 AATAATAATATGCTAA-AACAATAATAATATATA
* * * *
33659380 AATAATAATATGGTAAAATAATAATAATGTATT
1 AATAATAATATGCTAAAACAATAATAATATATA
33659413 AATAA
1 AATAA
33659418 GAATGATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 25 0.76
34 8 0.24
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.34
Consensus pattern (33 bp):
AATAATAATATGCTAAAACAATAATAATATATA
Found at i:33659385 original size:14 final size:16
Alignment explanation
Indices: 33659361--33659405 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
33659351 ATATATGCTA
33659361 ATAACAATAATAATAT-
1 ATAA-AATAATAATATG
33659377 AT-AAATAATAATATG
1 ATAAAATAATAATATG
*
33659392 GTAAAATAATAATA
1 ATAAAATAATAATA
33659406 ATGTATTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 11 0.42
15 2 0.08
16 13 0.50
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (16 bp):
ATAAAATAATAATATG
Found at i:33659436 original size:14 final size:15
Alignment explanation
Indices: 33659396--33659437 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
33659386 AATATGGTAA
*
33659396 AATAATAATAATG-T
1 AATAATAAGAATGAT
*
33659410 ATTAATAAGAATGAT
1 AATAATAAGAATGAT
33659425 AATAATAA-AATGA
1 AATAATAAGAATGA
33659438 GGTTATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.31
Consensus pattern (15 bp):
AATAATAAGAATGAT
Done.