Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 133 of 318
Found at i:40707651 original size:40 final size:38
Alignment explanation
Indices: 40707602--40707709 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
40707592 ATCACGATTT
*
40707602 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
40707642 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
40707682 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
40707710 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:40709677 original size:15 final size:17
Alignment explanation
Indices: 40709657--40709692 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
40709647 CTCATTTTTC
40709657 TTTTCA-TTTCT-TCCT
1 TTTTCATTTTCTCTCCT
40709672 TTTTCATTTTCTCTCCT
1 TTTTCATTTTCTCTCCT
40709689 TTTT
1 TTTT
40709693 GAAAAACAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 5 0.26
17 8 0.42
ACGTcount: A:0.06, C:0.25, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTCATTTTCTCTCCT
Found at i:40710703 original size:15 final size:15
Alignment explanation
Indices: 40710683--40710716 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
40710673 CATGAAAAAT
40710683 ATGATTTATGATG-TG
1 ATGATTTATG-TGATG
40710698 ATGATTTATGTGATG
1 ATGATTTATGTGATG
40710713 ATGA
1 ATGA
40710717 CATATGTGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 2 0.11
15 16 0.89
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.44
Consensus pattern (15 bp):
ATGATTTATGTGATG
Found at i:40711730 original size:50 final size:50
Alignment explanation
Indices: 40711649--40711747 Score: 153
Period size: 50 Copynumber: 2.0 Consensus size: 50
40711639 AATGATCGTT
* **
40711649 AAATGTTTTAAGAAAATTATTAGTCGTTGCAATTATGTTTTAAAAACTAG
1 AAATGTTTTAAGAAAATAATTAGTCAATGCAATTATGTTTTAAAAACTAG
* *
40711699 AAATGTTTTAAGAAAATAATTCGTCAATGCAATTGTGTTTTAAAAACTA
1 AAATGTTTTAAGAAAATAATTAGTCAATGCAATTATGTTTTAAAAACTA
40711748 AGTTATAATA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.38
Consensus pattern (50 bp):
AAATGTTTTAAGAAAATAATTAGTCAATGCAATTATGTTTTAAAAACTAG
Found at i:40720351 original size:28 final size:28
Alignment explanation
Indices: 40720296--40720408 Score: 144
Period size: 28 Copynumber: 4.1 Consensus size: 28
40720286 AGCATGGATG
* *
40720296 CCAG-AACAGATA-TTGTGACAGAGTCA
1 CCAGAAACAGATATTTGTGGCAGAGCCA
*
40720322 CCA-AATACAGATAATTGTGGCAG-GACCA
1 CCAGAA-ACAGATATTTGTGGCAGAG-CCA
*
40720350 CCAGAAATAGATATTTGTGGCAGAGCCA
1 CCAGAAACAGATATTTGTGGCAGAGCCA
40720378 CCAGAAACAGATATTTGTGGCAGAGCCA
1 CCAGAAACAGATATTTGTGGCAGAGCCA
40720406 CCA
1 CCA
40720409 AAATGCTTCC
Statistics
Matches: 76, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
26 4 0.05
27 8 0.11
28 61 0.80
29 3 0.04
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.19
Consensus pattern (28 bp):
CCAGAAACAGATATTTGTGGCAGAGCCA
Found at i:40721689 original size:18 final size:17
Alignment explanation
Indices: 40721638--40721692 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 17
40721628 ATTCGGCTAT
40721638 AGAGG-AAAAGAAGAAG
1 AGAGGAAAAAGAAGAAG
* * *
40721654 ATGATGAAATAGATGAAG
1 A-GAGGAAAAAGAAGAAG
40721672 AGAGGAAAAAAGAAGAAG
1 AGAGG-AAAAAGAAGAAG
40721690 AGA
1 AGA
40721693 AAAGAATTGT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
16 1 0.03
17 6 0.20
18 23 0.77
ACGTcount: A:0.60, C:0.00, G:0.33, T:0.07
Consensus pattern (17 bp):
AGAGGAAAAAGAAGAAG
Found at i:40728299 original size:28 final size:27
Alignment explanation
Indices: 40728243--40728332 Score: 119
Period size: 28 Copynumber: 3.3 Consensus size: 27
40728233 CAGCATGGCT
* *
40728243 ACCAGAACAGAT-ATTGTGACAGAGTC
1 ACCAGAACAGATAATTGTGGCAGAGCC
*
40728269 ACCAGATACAGATAATTGTGGCAGGGCC
1 ACCAGA-ACAGATAATTGTGGCAGAGCC
*
40728297 ACCAGAAACAGATATTTGTGGCAGAGCC
1 ACCAG-AACAGATAATTGTGGCAGAGCC
40728325 ACCAGAAC
1 ACCAGAAC
40728333 GCTTTCTCCA
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
26 6 0.11
27 9 0.16
28 40 0.71
29 1 0.02
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.17
Consensus pattern (27 bp):
ACCAGAACAGATAATTGTGGCAGAGCC
Found at i:40728615 original size:18 final size:18
Alignment explanation
Indices: 40728592--40728630 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
40728582 TAGGCCCGTT
40728592 GGCCCATTATCCCATTTC
1 GGCCCATTATCCCATTTC
*
40728610 GGCCCATTATCCCGTTTC
1 GGCCCATTATCCCATTTC
40728628 GGC
1 GGC
40728631 ATACCAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.13, C:0.38, G:0.18, T:0.31
Consensus pattern (18 bp):
GGCCCATTATCCCATTTC
Found at i:40729629 original size:18 final size:18
Alignment explanation
Indices: 40729582--40729632 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
40729572 AGCTGTAGAG
40729582 GAAAAGAAGAAGAAGAGGA
1 GAAAAGAAGAAG-AGAGGA
* *
40729601 -AATAGATGAAGAGAGGA
1 GAAAAGAAGAAGAGAGGA
40729618 GAAAAGAAGAAGAGA
1 GAAAAGAAGAAGAGA
40729633 AAAGAATTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 6 0.22
18 21 0.78
ACGTcount: A:0.61, C:0.00, G:0.35, T:0.04
Consensus pattern (18 bp):
GAAAAGAAGAAGAGAGGA
Found at i:40729638 original size:18 final size:18
Alignment explanation
Indices: 40729582--40729638 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
40729572 AGCTGTAGAG
*
40729582 GAAAAGAAGAAGA-AGAG
1 GAAAAGAAGAAGAGAGAA
* *
40729599 GAAATAGATGAAGAGAGGA
1 GAAA-AGAAGAAGAGAGAA
*
40729618 GAAAAGAAGAAGAGAAAA
1 GAAAAGAAGAAGAGAGAA
40729636 GAA
1 GAA
40729639 TTGTCAGAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
17 4 0.12
18 22 0.69
19 6 0.19
ACGTcount: A:0.63, C:0.00, G:0.33, T:0.04
Consensus pattern (18 bp):
GAAAAGAAGAAGAGAGAA
Found at i:40735959 original size:40 final size:40
Alignment explanation
Indices: 40735866--40736083 Score: 266
Period size: 40 Copynumber: 5.5 Consensus size: 40
40735856 AAGCCAAGTA
* * *
40735866 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTC-AATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
40735904 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
40735944 CCTTCGGAACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
40735984 CCTTCGGGACTTAGCCCGGATGTAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
40736024 CCTTCGAGACTTAGCCCGGA-ACTAGTCACTAGCGTA-AAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACT--CGCACAAATG
40736065 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
40736084 TTATCATCCA
Statistics
Matches: 158, Mismatches: 16, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
38 12 0.08
39 17 0.11
40 103 0.65
41 23 0.15
42 3 0.02
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:40743407 original size:42 final size:43
Alignment explanation
Indices: 40743311--40743422 Score: 145
Period size: 43 Copynumber: 2.6 Consensus size: 43
40743301 CAATGCGATC
** * * *
40743311 GTCCCAAATGTGGTCTTACATGAAATCAAATATTGATGCCACT
1 GTCCCAAACATGGTCTTACACGAAATCAAATATCGATGCCAAT
* *
40743354 GTCCCAGACATGGTCTTACACGAAATCATATA-CGATGCCAAT
1 GTCCCAAACATGGTCTTACACGAAATCAAATATCGATGCCAAT
40743396 GTCCCAAACATGGTCTTACACGTAAAT
1 GTCCCAAACATGGTCTTACACG-AAAT
40743423 AACAAATCAA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
42 29 0.48
43 31 0.52
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (43 bp):
GTCCCAAACATGGTCTTACACGAAATCAAATATCGATGCCAAT
Found at i:40745732 original size:19 final size:19
Alignment explanation
Indices: 40745708--40745752 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
40745698 AGTTATTCGA
*
40745708 GCTTACTAAGCATGAAAAT
1 GCTTACCAAGCATGAAAAT
*
40745727 GCTTACCCAGCATGAAAAT
1 GCTTACCAAGCATGAAAAT
40745746 GCTTACC
1 GCTTACC
40745753 CCTCCCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (19 bp):
GCTTACCAAGCATGAAAAT
Found at i:40745753 original size:19 final size:19
Alignment explanation
Indices: 40745716--40745753 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
40745706 GAGCTTACTA
40745716 AGCATGAAAATGCTTACCC
1 AGCATGAAAATGCTTACCC
40745735 AGCATGAAAATGCTTACCC
1 AGCATGAAAATGCTTACCC
40745754 CTCCCTTTTT
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:0.37, C:0.26, G:0.16, T:0.21
Consensus pattern (19 bp):
AGCATGAAAATGCTTACCC
Found at i:40747148 original size:27 final size:26
Alignment explanation
Indices: 40747100--40747159 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
40747090 GCAAAGCTGC
*
40747100 CAGATATTGTGACAAAGTCACCAGATA
1 CAGATATTGTGACAAAGCCACCAGA-A
* * *
40747127 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACAAAGCCACCAGAA
40747153 CAGATAT
1 CAGATAT
40747160 ATATATGTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACAAAGCCACCAGAA
Found at i:40751798 original size:26 final size:26
Alignment explanation
Indices: 40751769--40751821 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
40751759 CATGCAGCAT
40751769 ATGAATGGGTAAATCCAACATCTATC
1 ATGAATGGGTAAATCCAACATCTATC
*
40751795 ATGAATGGGTAGATCCAACATCTATC
1 ATGAATGGGTAAATCCAACATCTATC
40751821 A
1 A
40751822 ACGCAGTGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (26 bp):
ATGAATGGGTAAATCCAACATCTATC
Found at i:40754429 original size:26 final size:25
Alignment explanation
Indices: 40754382--40754430 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
40754372 GCGAAGCTGC
*
40754382 CAGATATTGTGACGAAGTCACCAAA
1 CAGATATTGTGACGAAGCCACCAAA
* *
40754407 CAGATATATGTGGCGAGGCCACCA
1 CAGATAT-TGTGACGAAGCCACCA
40754431 TATTACAGCG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 7 0.35
26 13 0.65
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.18
Consensus pattern (25 bp):
CAGATATTGTGACGAAGCCACCAAA
Found at i:40759535 original size:25 final size:25
Alignment explanation
Indices: 40759506--40759555 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
40759496 GGTAGGAAGT
40759506 GCCGAACTCCATTGTACTGGACAGA
1 GCCGAACTCCATTGTACTGGACAGA
40759531 GCCGAACTCCATTGTACTGGACAGA
1 GCCGAACTCCATTGTACTGGACAGA
40759556 ACTCAAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.20
Consensus pattern (25 bp):
GCCGAACTCCATTGTACTGGACAGA
Found at i:40761006 original size:93 final size:93
Alignment explanation
Indices: 40760894--40761064 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
40760884 GCCCCTAAGT
*
40760894 GAACTCGGACTCAACTCAACGAGCTC-GAGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCGGA-CATTCGCATCCATAAGTGAACTCGGACTCAACTCA
40760958 ACGAGTTCGGATGCCTAGTTACATCTCAC
65 ACGAGTTCGGATGCCTAGTTACATCTCAC
*
40760987 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40761052 CGAGTTCGGATGC
66 CGAGTTCGGATGC
40761065 TCAACCATCC
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
93 73 0.97
94 2 0.03
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:40761060 original size:46 final size:47
Alignment explanation
Indices: 40760889--40761061 Score: 223
Period size: 46 Copynumber: 3.7 Consensus size: 47
40760879 AACCCGCCCC
* *
40760889 TAAGTGAACTCGGACTCAACTCAACGAGCTC-GAGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTCGCATCCA
*
40760935 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA-G-C-A-TTCGCATCCA
* *
40760983 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA-CATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTCGCATCCA
40761028 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40761062 TGCTCAACCA
Statistics
Matches: 110, Mismatches: 8, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 59 0.54
47 31 0.28
48 3 0.03
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.21
Consensus pattern (47 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTCGCATCCA
Found at i:40761517 original size:30 final size:30
Alignment explanation
Indices: 40761483--40761542 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
40761473 ATTTAATACG
40761483 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
40761513 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
40761543 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:40768556 original size:47 final size:49
Alignment explanation
Indices: 40768439--40768613 Score: 183
Period size: 46 Copynumber: 3.8 Consensus size: 49
40768429 AACCCGCCCC
* * * *
40768439 TAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-CGTTCGCATCCA
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACATCCA
*
40768485 TAA-TGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A-TTCACATCCA
* *
40768532 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTCGCATCCA
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACATCCA
*
40768577 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGC
40768614 TCAACCATCC
Statistics
Matches: 109, Mismatches: 8, Indels: 21
0.79 0.06 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 30 0.28
46 32 0.29
47 32 0.29
48 2 0.02
49 3 0.03
50 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (49 bp):
TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACATCCA
Found at i:40769066 original size:30 final size:30
Alignment explanation
Indices: 40769032--40769091 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
40769022 ATTTAATACG
40769032 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
40769062 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
40769092 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:40776449 original size:67 final size:67
Alignment explanation
Indices: 40776375--40776523 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
40776365 CATCATGTGT
* * *
40776375 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATG-GT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
40776436 ATGTAG
62 ATGTAG
** * *
40776442 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
40776507 AG
66 AG
40776509 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
40776524 GATAAACTGG
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
63 18 0.26
64 5 0.07
65 6 0.09
66 2 0.03
67 39 0.56
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:40776479 original size:63 final size:63
Alignment explanation
Indices: 40776399--40776581 Score: 183
Period size: 63 Copynumber: 2.8 Consensus size: 63
40776389 AGACATTATG
* *
40776399 ATGTAGCTAGGTCGCATGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
40776462 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATG-GT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
40776527 AA
62 AA
* * * *
40776529 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCAT-GGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
40776582 CGAACTATAT
Statistics
Matches: 98, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
62 1 0.01
63 37 0.38
64 3 0.03
65 8 0.08
66 15 0.15
67 32 0.33
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (63 bp):
ATGTAGCTAGGTCGCATGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:40780350 original size:27 final size:27
Alignment explanation
Indices: 40780312--40780555 Score: 308
Period size: 27 Copynumber: 9.0 Consensus size: 27
40780302 GGTCATTATT
* *
40780312 TGACCGTCATGCCGCTGTAGGGTAAAA
1 TGACCGTAATGCCCCTGTAGGGTAAAA
* *
40780339 TGACCGTAATGCCGCTGTAGTGTAAAA
1 TGACCGTAATGCCCCTGTAGGGTAAAA
* *
40780366 TGACCGTAATACCCCTGTAAGGTAAAA
1 TGACCGTAATGCCCCTGTAGGGTAAAA
* *
40780393 TGACCGTAATACCCCTGTAGAGTAAAA
1 TGACCGTAATGCCCCTGTAGGGTAAAA
*
40780420 TAACCGTAATGCCCCTGTAGGGTAAAA
1 TGACCGTAATGCCCCTGTAGGGTAAAA
* *
40780447 TGACCATAATGCCCCTGTTGGGTAAAA
1 TGACCGTAATGCCCCTGTAGGGTAAAA
* * *
40780474 TCATCGTAATGCCCCTGTAGAGTAAAA
1 TGACCGTAATGCCCCTGTAGGGTAAAA
* * *
40780501 TGACCGTAATGCCTCTGTAGGGTGATA
1 TGACCGTAATGCCCCTGTAGGGTAAAA
* * *
40780528 TGACCGTAATACCCTTGTATGGTAAAA
1 TGACCGTAATGCCCCTGTAGGGTAAAA
40780555 T
1 T
40780556 CACGATTATG
Statistics
Matches: 186, Mismatches: 31, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 186 1.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (27 bp):
TGACCGTAATGCCCCTGTAGGGTAAAA
Found at i:40780755 original size:27 final size:27
Alignment explanation
Indices: 40780698--40780755 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
40780688 GAAAGTTTTG
* * * *
40780698 TACTGGTGACTATGTCACATTTATTGT
1 TACTGGTGACTATGCCACAATTACTGA
**
40780725 TACTGGTGGGTATGCCACAATTACTGA
1 TACTGGTGACTATGCCACAATTACTGA
40780752 TACT
1 TACT
40780756 AATGGCTTTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (27 bp):
TACTGGTGACTATGCCACAATTACTGA
Found at i:40780985 original size:28 final size:30
Alignment explanation
Indices: 40780945--40781030 Score: 79
Period size: 33 Copynumber: 2.8 Consensus size: 30
40780935 ACTGTATTGT
* * *
40780945 TACTGCATTGGGCTTAGGCCCATAC-TGC-
1 TACTGAATAGGGCTTAGGCCCAGACATGCA
*
40780973 TACTGTATAGGGC-TAGGGCCCAGACTATGCAGA
1 TACTGAATAGGGCTTA-GGCCCAGAC-ATGC--A
40781006 TACTGAATAGGGCTTAGGCCCAGAC
1 TACTGAATAGGGCTTAGGCCCAGAC
40781031 TATGTTATTC
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
27 2 0.04
28 19 0.40
30 3 0.06
33 21 0.45
34 2 0.04
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.23
Consensus pattern (30 bp):
TACTGAATAGGGCTTAGGCCCAGACATGCA
Found at i:40784631 original size:27 final size:27
Alignment explanation
Indices: 40784587--40784803 Score: 233
Period size: 27 Copynumber: 8.1 Consensus size: 27
40784577 GGTTCTTATT
* *
40784587 TGACCATAATGCCACTGTAGGGTAAAA
1 TGACCATAATACCCCTGTAGGGTAAAA
40784614 TGACCATAATACCCCTGTAGGGTAAAA
1 TGACCATAATACCCCTGTAGGGTAAAA
* *
40784641 TGACCATAATACCACTGTAGAGTAAAA
1 TGACCATAATACCCCTGTAGGGTAAAA
** * *
40784668 TGACTGTAAT--GCCTTTAGGGT-AAA
1 TGACCATAATACCCCTGTAGGGTAAAA
* ** *
40784692 TGACCGTAATTTCCCTGTAGGGTAAAG
1 TGACCATAATACCCCTGTAGGGTAAAA
* *
40784719 TGACCATAATGCCCCTGTAGAGTAAAA
1 TGACCATAATACCCCTGTAGGGTAAAA
* * *
40784746 TGATCGTAATGCCCCTGTAGGGTAAAA
1 TGACCATAATACCCCTGTAGGGTAAAA
* * *
40784773 TGACCGTAATACCCTTGTATGGTAAAA
1 TGACCATAATACCCCTGTAGGGTAAAA
40784800 TGAC
1 TGAC
40784804 GATTATTCCT
Statistics
Matches: 161, Mismatches: 26, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
24 12 0.07
25 7 0.04
26 9 0.06
27 133 0.83
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (27 bp):
TGACCATAATACCCCTGTAGGGTAAAA
Found at i:40784737 original size:78 final size:80
Alignment explanation
Indices: 40784593--40784803 Score: 293
Period size: 78 Copynumber: 2.6 Consensus size: 80
40784583 TATTTGACCA
*
40784593 TAATGCCACTGTAGGGTAAAATGACCATAATACCCCTGTAGGGTAAAATGACCATAATACCACTG
1 TAATGCC-CTGTAGGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCATAATACCACTG
40784658 TAGAGTAAAATGA-CTG
65 TAGAGTAAAATGATC-G
* ** * * *
40784674 TAATG-CCTTTAGGGT-AAATGACCGTAATTTCCCTGTAGGGTAAAGTGACCATAATGCCCCTGT
1 TAATGCCCTGTAGGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCATAATACCACTGT
40784737 AGAGTAAAATGATCG
66 AGAGTAAAATGATCG
* *
40784752 TAATGCCCCTGTAGGGTAAAATGACCGTAATACCCTTGTATGGTAAAATGAC
1 TAATG-CCCTGTAGGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGAC
40784804 GATTATTCCT
Statistics
Matches: 113, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
78 60 0.53
79 9 0.08
80 10 0.09
81 34 0.30
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (80 bp):
TAATGCCCTGTAGGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCATAATACCACTGT
AGAGTAAAATGATCG
Found at i:40784982 original size:27 final size:26
Alignment explanation
Indices: 40784943--40785024 Score: 92
Period size: 27 Copynumber: 3.0 Consensus size: 26
40784933 GGAAGTTCTG
* *
40784943 TACTGGTGACTATGTCACATTCACTGT
1 TACTGGTGGCTATGCCACATT-ACTGT
* *
40784970 TACTAGTGGCTATGCCACAATTACTGA
1 TACTGGTGGCTATGCCAC-ATTACTGT
*
40784997 TACTGGTGGCTTTGCCACATTTACTGT
1 TACTGGTGGCTATGCCACA-TTACTGT
40785024 T
1 T
40785025 TTTGGTAGCT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
26 1 0.02
27 42 0.91
28 3 0.07
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37
Consensus pattern (26 bp):
TACTGGTGGCTATGCCACATTACTGT
Found at i:40786778 original size:39 final size:39
Alignment explanation
Indices: 40786715--40786833 Score: 166
Period size: 39 Copynumber: 3.1 Consensus size: 39
40786705 TGTGAATATA
* *
40786715 TATACGCGAGAATTATATCTGGACTTCAGGTCCGCAAGC
1 TATAAGCGAGAATTATATCTGGACTTCAGGTCCGCAGGC
* * *
40786754 TATAAGCGAGAATTATATCCGGACTTCATGTCTGCAGGC
1 TATAAGCGAGAATTATATCTGGACTTCAGGTCCGCAGGC
* * *
40786793 TATATGAGAGAATTATATCTGGACTTTAGGTCCGCAGGC
1 TATAAGCGAGAATTATATCTGGACTTCAGGTCCGCAGGC
40786832 TA
1 TA
40786834 CGTGCTGGAC
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 69 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (39 bp):
TATAAGCGAGAATTATATCTGGACTTCAGGTCCGCAGGC
Found at i:40788266 original size:203 final size:203
Alignment explanation
Indices: 40787911--40788320 Score: 766
Period size: 203 Copynumber: 2.0 Consensus size: 203
40787901 CCATATGAGC
40787911 CGTATTTTATGAGATGTTTAAGTTTTCGTGAAACAGGACCAGAGCGATTTCTAGATCCCCTGTTC
1 CGTATTTTATGAGATGTTTAAGTTTTCGTGAAACAGGACCAGAGCGATTTCTAGATCCCCTGTTC
*
40787976 TGACTTTGGAAATTCACCATAAATTAACCAGAGATAATTAGAAGTCATGCTTTATATGTACAGAC
66 TAACTTTGGAAATTCACCATAAATTAACCAGAGATAATTAGAAGTCATGCTTTATATGTACAGAC
*
40788041 TCCTTTTTGAGTCTAGTTTCATTAGAAACAAATGGCATAAGTGTTGAAGCCCTGTACAAGGATAT
131 TCCTTTTTGAGTCTAATTTCATTAGAAACAAATGGCATAAGTGTTGAAGCCCTGTACAAGGATAT
40788106 ATCTAAGT
196 ATCTAAGT
* * *
40788114 CGTATTTTATGAGATGTTTAAGTTTTTGTGAAACAGGACTAGAGCGATTTCTGGATCCCCTGTTC
1 CGTATTTTATGAGATGTTTAAGTTTTCGTGAAACAGGACCAGAGCGATTTCTAGATCCCCTGTTC
*
40788179 TAACTTTGGAAATTCACCATAAATTAACTAGAGATAATTAGAAGTCATGCTTTATATGTACAGAC
66 TAACTTTGGAAATTCACCATAAATTAACCAGAGATAATTAGAAGTCATGCTTTATATGTACAGAC
40788244 TCCTTTTTGAGTCTAATTTCATTAGAAACAAATGGCATAAGTGTTGAAGCCCTGTACAAGGATAT
131 TCCTTTTTGAGTCTAATTTCATTAGAAACAAATGGCATAAGTGTTGAAGCCCTGTACAAGGATAT
40788309 ATCTAAGT
196 ATCTAAGT
40788317 CGTA
1 CGTA
40788321 ATGCATGAAG
Statistics
Matches: 201, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
203 201 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Consensus pattern (203 bp):
CGTATTTTATGAGATGTTTAAGTTTTCGTGAAACAGGACCAGAGCGATTTCTAGATCCCCTGTTC
TAACTTTGGAAATTCACCATAAATTAACCAGAGATAATTAGAAGTCATGCTTTATATGTACAGAC
TCCTTTTTGAGTCTAATTTCATTAGAAACAAATGGCATAAGTGTTGAAGCCCTGTACAAGGATAT
ATCTAAGT
Found at i:40795130 original size:77 final size:77
Alignment explanation
Indices: 40795042--40795197 Score: 242
Period size: 77 Copynumber: 2.0 Consensus size: 77
40795032 TGTGAATATA
*
40795042 TATACGCGAGAAATATATCTGGACTTCAGGTCCGCAGGCTA-AAGTGAGAATTATATCCGGACTT
1 TATACGCGAGAAATATATC-GGACTTCAGGTCCGCAGGCTATAAGCGAGAATTATATCCGGACTT
40795106 CAGGTCCGCAGGC
65 CAGGTCCGCAGGC
* * * * *
40795119 TATATGCGAGAATTATATCGGACTTCATGTCCGCAGGCTATATGCGAGAATTATATCCGGACTTT
1 TATACGCGAGAAATATATCGGACTTCAGGTCCGCAGGCTATAAGCGAGAATTATATCCGGACTTC
40795184 AGGTCCGCAGGC
66 AGGTCCGCAGGC
40795196 TA
1 TA
40795198 CGTGCTGGAC
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
76 20 0.28
77 52 0.72
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (77 bp):
TATACGCGAGAAATATATCGGACTTCAGGTCCGCAGGCTATAAGCGAGAATTATATCCGGACTTC
AGGTCCGCAGGC
Found at i:40795213 original size:77 final size:76
Alignment explanation
Indices: 40795047--40795216 Score: 227
Period size: 77 Copynumber: 2.2 Consensus size: 76
40795037 ATATATATAC
*
40795047 GCGAGAAATATATCTGGACTTCAGGTCCGCAGGCTAAAGTGAGAATTATATCCGGACTTCAGGTC
1 GCGAG-AATATATCTGGACTTCAGGTCCGCAGGCTAAAGCGAGAATTATATCCGGACTTCAGGTC
*
40795112 CGCAGGCTATAT
65 CGCAGGCTACAT
* * *
40795124 GCGAGAATTATATC-GGACTTCATGTCCGCAGGCTATATGCGAGAATTATATCCGGACTTTAGGT
1 GCGAGAA-TATATCTGGACTTCAGGTCCGCAGGCTA-AAGCGAGAATTATATCCGGACTTCAGGT
*
40795188 CCGCAGGCTACGT
64 CCGCAGGCTACAT
40795201 GCTG-GACATATATCTG
1 GC-GAGA-ATATATCTG
40795217 AATTTAAAGT
Statistics
Matches: 82, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
76 22 0.27
77 57 0.70
78 3 0.04
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (76 bp):
GCGAGAATATATCTGGACTTCAGGTCCGCAGGCTAAAGCGAGAATTATATCCGGACTTCAGGTCC
GCAGGCTACAT
Found at i:40795214 original size:39 final size:39
Alignment explanation
Indices: 40795042--40795197 Score: 235
Period size: 38 Copynumber: 4.1 Consensus size: 39
40795032 TGTGAATATA
* * *
40795042 TATACGCGAGAAATATATCTGGACTTCAGGTCCGCAGGC
1 TATATGCGAGAATTATATCCGGACTTCAGGTCCGCAGGC
* *
40795081 TA-AAGTGAGAATTATATCCGGACTTCAGGTCCGCAGGC
1 TATATGCGAGAATTATATCCGGACTTCAGGTCCGCAGGC
*
40795119 TATATGCGAGAATTATAT-CGGACTTCATGTCCGCAGGC
1 TATATGCGAGAATTATATCCGGACTTCAGGTCCGCAGGC
*
40795157 TATATGCGAGAATTATATCCGGACTTTAGGTCCGCAGGC
1 TATATGCGAGAATTATATCCGGACTTCAGGTCCGCAGGC
40795196 TA
1 TA
40795198 CGTGCTGGAC
Statistics
Matches: 106, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
38 71 0.67
39 35 0.33
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (39 bp):
TATATGCGAGAATTATATCCGGACTTCAGGTCCGCAGGC
Found at i:40801305 original size:21 final size:21
Alignment explanation
Indices: 40801281--40801322 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
40801271 TCATCAGATC
*
40801281 TACACCTTGAGGCATCGGGGG
1 TACACCTTGAGGAATCGGGGG
**
40801302 TACAGGTTGAGGAATCGGGGG
1 TACACCTTGAGGAATCGGGGG
40801323 AGTGGGGGAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.17, G:0.43, T:0.19
Consensus pattern (21 bp):
TACACCTTGAGGAATCGGGGG
Found at i:40806379 original size:16 final size:16
Alignment explanation
Indices: 40806358--40806400 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
40806348 GTAGATCGGC
40806358 AAAAGTCGAAATGCCG
1 AAAAGTCGAAATGCCG
*
40806374 AAAAGTCGAAATGCTG
1 AAAAGTCGAAATGCCG
*
40806390 AAAAGCCGAAA
1 AAAAGTCGAAA
40806401 GTTTGGCTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.49, C:0.16, G:0.23, T:0.12
Consensus pattern (16 bp):
AAAAGTCGAAATGCCG
Found at i:40806658 original size:28 final size:28
Alignment explanation
Indices: 40806615--40806715 Score: 114
Period size: 28 Copynumber: 3.6 Consensus size: 28
40806605 GCATGACGGC
**
40806615 AAATGTGATTGGGCCTAAT-AGCCGTAT
1 AAATGTGATTGGGCCTAATGAGCCACAT
*
40806642 AAATGTGACTTGGGCCTAATGGGCCACAT
1 AAATGTGA-TTGGGCCTAATGAGCCACAT
* *
40806671 AAATGTGATTGGGCCTAATGCGCCATAT
1 AAATGTGATTGGGCCTAATGAGCCACAT
* * *
40806699 GAAGGAGATTGGGCCTA
1 AAATGTGATTGGGCCTA
40806716 GTGCGCGATA
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
27 8 0.12
28 43 0.67
29 13 0.20
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.26
Consensus pattern (28 bp):
AAATGTGATTGGGCCTAATGAGCCACAT
Found at i:40813964 original size:16 final size:16
Alignment explanation
Indices: 40813943--40813985 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
40813933 GTAGATCGGT
*
40813943 AAAAGCCGAAATGCTG
1 AAAAGCCGAAATGCCG
40813959 AAAAGCCGAAATGCCG
1 AAAAGCCGAAATGCCG
40813975 AAAAGCCGAAA
1 AAAAGCCGAAA
40813986 GTTTGGCTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.49, C:0.21, G:0.23, T:0.07
Consensus pattern (16 bp):
AAAAGCCGAAATGCCG
Found at i:40813969 original size:8 final size:8
Alignment explanation
Indices: 40813943--40813985 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
40813933 GTAGATCGGT
40813943 AAAAGCCG
1 AAAAGCCG
* *
40813951 AAATGCTG
1 AAAAGCCG
40813959 AAAAGCCG
1 AAAAGCCG
*
40813967 AAATGCCG
1 AAAAGCCG
40813975 AAAAGCCG
1 AAAAGCCG
40813983 AAA
1 AAA
40813986 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.49, C:0.21, G:0.23, T:0.07
Consensus pattern (8 bp):
AAAAGCCG
Found at i:40814262 original size:29 final size:27
Alignment explanation
Indices: 40814199--40814274 Score: 89
Period size: 29 Copynumber: 2.7 Consensus size: 27
40814189 AGCATAACGG
* **
40814199 TAAATGTGATTAGGCCTAATGGCCGTA
1 TAAATGTGATTTGGCCTAATGGCCACA
40814226 TAAATGTGATTTGGACCTAATGGGCCACA
1 TAAATGTGATTTGG-CCTAAT-GGCCACA
* *
40814255 TAATTGTGATTGGGCCTAAT
1 TAAATGTGATTTGGCCTAAT
40814275 TTGCCATATG
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 13 0.31
28 12 0.29
29 17 0.40
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (27 bp):
TAAATGTGATTTGGCCTAATGGCCACA
Found at i:40814280 original size:28 final size:28
Alignment explanation
Indices: 40814199--40814280 Score: 85
Period size: 28 Copynumber: 2.9 Consensus size: 28
40814189 AGCATAACGG
* **
40814199 TAAATGTGATTAGGCCTAA-TGGCCGTA
1 TAAATGTGATTGGGCCTAATTGGCCACA
* *
40814226 TAAATGTGATTTGGACCTAATGGGCCACA
1 TAAATGTGA-TTGGGCCTAATTGGCCACA
* *
40814255 TAATTGTGATTGGGCCTAATTTGCCA
1 TAAATGTGATTGGGCCTAATTGGCCA
40814281 TATGGAGGAG
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
27 9 0.20
28 22 0.50
29 13 0.30
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (28 bp):
TAAATGTGATTGGGCCTAATTGGCCACA
Found at i:40816393 original size:28 final size:29
Alignment explanation
Indices: 40816326--40816426 Score: 125
Period size: 28 Copynumber: 3.5 Consensus size: 29
40816316 ATAGTGAATC
*
40816326 CGCACACTTAGTGCTATATACATTC-AGCT
1 CGCACACTTAGTGCTATATA-ATTCAAACT
40816355 CGCACACTTAGTGCTATATAA-TCAAACT
1 CGCACACTTAGTGCTATATAATTCAAACT
* * * *
40816383 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA-TTCAAACT
40816413 CGCACACTTAGTGC
1 CGCACACTTAGTGC
40816427 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.03
28 23 0.36
29 20 0.31
30 19 0.30
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATAATTCAAACT
Found at i:40827864 original size:40 final size:39
Alignment explanation
Indices: 40827699--40827882 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
40827689 AAATTGAATG
* * *
40827699 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
40827739 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
40827779 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
40827819 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
40827858 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
40827883 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:40827907 original size:80 final size:81
Alignment explanation
Indices: 40827739--40827927 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
40827729 GCTGGAAATT
* * * *
40827739 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
40827804 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
40827820 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
40827883 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
40827899 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
40827928 ATCGAGTAGC
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:40831491 original size:2 final size:2
Alignment explanation
Indices: 40831484--40831512 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
40831474 TCAATTCATA
40831484 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40831513 ACATGCGTTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40833046 original size:48 final size:47
Alignment explanation
Indices: 40832909--40833089 Score: 156
Period size: 48 Copynumber: 3.9 Consensus size: 47
40832899 AGGTTATGTA
* * * * *
40832909 TAATCCTATGTAAGACCATGTCTGGGACATGACTTTGTCATCAATATG
1 TAATCCCATGTAAGACCATGTTTGGGACATGA-ATTGGCATCGATATG
** * * *
40832957 TAATTTCGTGTAAGACCATAG-GTGGG-C-T--ATCGGCATCGATATG
1 TAATCCCATGTAAGACCAT-GTTTGGGACATGAATTGGCATCGATATG
40833000 TAATCCCATGTAAGACCATGTTTGGGACATGGAATTGGCATCGATATG
1 TAATCCCATGTAAGACCATGTTTGGGACAT-GAATTGGCATCGATATG
* * * * *
40833048 TGATCCCATGTAAGTCCATATTTGGGATATGGCATTGGCATC
1 TAATCCCATGTAAGACCATGTTTGGGACAT-GAATTGGCATC
40833090 CTACCATGTG
Statistics
Matches: 107, Mismatches: 19, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
42 1 0.01
43 31 0.29
44 1 0.01
45 1 0.01
46 1 0.01
47 1 0.01
48 70 0.65
49 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (47 bp):
TAATCCCATGTAAGACCATGTTTGGGACATGAATTGGCATCGATATG
Found at i:40848706 original size:47 final size:47
Alignment explanation
Indices: 40848584--40848713 Score: 144
Period size: 46 Copynumber: 2.8 Consensus size: 47
40848574 TGTAACCCGC
*
40848584 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGG-GCGTTCACAT
1 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGAGCGTTCACAT
* *
40848630 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGA-G-C--GTTCACAT
* *
40848680 -C-TCA-CGAACTCAGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGA
40848714 ACTCAACCAT
Statistics
Matches: 74, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
46 35 0.47
47 27 0.36
48 3 0.04
49 2 0.03
50 4 0.05
51 3 0.04
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.20
Consensus pattern (47 bp):
CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGAGCGTTCACAT
Found at i:40866156 original size:47 final size:47
Alignment explanation
Indices: 40866034--40866163 Score: 144
Period size: 46 Copynumber: 2.8 Consensus size: 47
40866024 TGTAACCCGC
*
40866034 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGG-GCGTTCACAT
1 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGAGCGTTCACAT
* *
40866080 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGA-G-C--GTTCACAT
* *
40866130 -C-TCA-CGAACTCAGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGA
40866164 ACTCAACCAT
Statistics
Matches: 74, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
46 35 0.47
47 27 0.36
48 3 0.04
49 2 0.03
50 4 0.05
51 3 0.04
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.20
Consensus pattern (47 bp):
CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGAGCGTTCACAT
Found at i:40877041 original size:49 final size:49
Alignment explanation
Indices: 40876968--40877213 Score: 321
Period size: 49 Copynumber: 5.0 Consensus size: 49
40876958 GTAGCTGAAG
* * * *
40876968 CTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAA
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCAA
*
40877017 TTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAA
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC-AA
* * * *
40877067 CCATTTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAA
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA
* * * * * *
40877117 GTTATCAGGTACGCATAGTAGCCTACACTTAGTACTACACATGTGACCAA
1 -CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCAA
*
40877167 CAATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC
40877214 TCACAATAGC
Statistics
Matches: 167, Mismatches: 27, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
49 82 0.49
50 48 0.29
51 37 0.22
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (49 bp):
CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCAA
Found at i:40877895 original size:30 final size:30
Alignment explanation
Indices: 40877861--40877920 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
40877851 CTTTAATACG
40877861 AACTTTGGCAAAATTAC-CATTCTGCCCCTA
1 AACTTTGGCAAAATTACAC-TTCTGCCCCTA
* * *
40877891 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTCTGCCCCTA
40877921 GGCTTGGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.28, C:0.28, G:0.08, T:0.35
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTCTGCCCCTA
Found at i:40879753 original size:27 final size:27
Alignment explanation
Indices: 40879699--40879809 Score: 145
Period size: 27 Copynumber: 4.1 Consensus size: 27
40879689 AGCATGGCTG
*
40879699 CCAGAACAGATAA-TGTGACAGAGTCA
1 CCAGAACAGATAATTGTGACAGAGCCA
*
40879725 CCAGAACAGATAATTGTGGCAGAGCCA
1 CCAGAACAGATAATTGTGACAGAGCCA
*
40879752 CCAGAACAGAT-ATATGTGGCAGAGCCA
1 CCAGAACAGATAAT-TGTGACAGAGCCA
* * *
40879779 CCAGATCAGATAAATGTGACATAGCCA
1 CCAGAACAGATAATTGTGACAGAGCCA
40879806 CCAG
1 CCAG
40879810 GACGCTTCCT
Statistics
Matches: 76, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
26 15 0.20
27 60 0.79
28 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.15
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGACAGAGCCA
Found at i:40881765 original size:40 final size:40
Alignment explanation
Indices: 40881672--40881889 Score: 275
Period size: 40 Copynumber: 5.5 Consensus size: 40
40881662 AAGCCAAGTA
* * *
40881672 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTC-AATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
40881710 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
40881750 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
40881790 CCTTCGGGACTTAGCCCGGATGTAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
40881830 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGTA-AAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACT--CGCACAAATG
40881871 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
40881890 TTATCATCCA
Statistics
Matches: 160, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
38 12 0.08
39 17 0.11
40 104 0.65
41 24 0.15
42 3 0.02
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:40890944 original size:40 final size:40
Alignment explanation
Indices: 40890850--40890994 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
40890840 TACTCGAATG
*
40890850 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
40890891 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
40890931 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
40890971 ATATCCGGGCTAAGACCTGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
40890995 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.67
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:40893109 original size:40 final size:40
Alignment explanation
Indices: 40893016--40893233 Score: 275
Period size: 40 Copynumber: 5.5 Consensus size: 40
40893006 AAGCCAAGTA
* * *
40893016 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTC-AATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
40893054 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
40893094 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
40893134 CCTTCGGGACTTAGCCCGGATGTAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
40893174 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGTA-AAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACT--CGCACAAATG
40893215 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
40893234 TTATCATCCA
Statistics
Matches: 160, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
38 12 0.08
39 17 0.11
40 104 0.65
41 24 0.15
42 3 0.02
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:40895951 original size:24 final size:24
Alignment explanation
Indices: 40895916--40895969 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
40895906 CCAACACTAT
*
40895916 TCTCCCTAATCAGCTCCTAAATCC
1 TCTCCCTAATCAGCTCCCAAATCC
* *
40895940 TCTCCCTTATCAGCTCCCAAATCT
1 TCTCCCTAATCAGCTCCCAAATCC
40895964 TCTCCC
1 TCTCCC
40895970 GACAGCCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.44, G:0.04, T:0.31
Consensus pattern (24 bp):
TCTCCCTAATCAGCTCCCAAATCC
Found at i:40902291 original size:27 final size:27
Alignment explanation
Indices: 40902237--40902347 Score: 145
Period size: 27 Copynumber: 4.1 Consensus size: 27
40902227 AGCATGGCTG
*
40902237 CCAGAACAGATAA-TGTGACAGAGTCA
1 CCAGAACAGATAATTGTGACAGAGCCA
*
40902263 CCAGAACAGATAATTGTGGCAGAGCCA
1 CCAGAACAGATAATTGTGACAGAGCCA
*
40902290 CCAGAACAGAT-ATATGTGGCAGAGCCA
1 CCAGAACAGATAAT-TGTGACAGAGCCA
* * *
40902317 CCAGATCAGATAAATGTGACATAGCCA
1 CCAGAACAGATAATTGTGACAGAGCCA
40902344 CCAG
1 CCAG
40902348 GACGCTTCCT
Statistics
Matches: 76, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
26 15 0.20
27 60 0.79
28 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.15
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGACAGAGCCA
Found at i:40903811 original size:24 final size:24
Alignment explanation
Indices: 40903776--40903852 Score: 118
Period size: 24 Copynumber: 3.2 Consensus size: 24
40903766 CCAACACTGT
*
40903776 TCTCCCTAATCAGCTCCTAAATCC
1 TCTCCCTTATCAGCTCCTAAATCC
40903800 TCTCCCTTATCAGCTCCTAAATCC
1 TCTCCCTTATCAGCTCCTAAATCC
* * *
40903824 TCTCTCTTATCAGCTCCCAAATCT
1 TCTCCCTTATCAGCTCCTAAATCC
40903848 TCTCC
1 TCTCC
40903853 TGACAGCCTT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.21, C:0.42, G:0.04, T:0.34
Consensus pattern (24 bp):
TCTCCCTTATCAGCTCCTAAATCC
Found at i:40905948 original size:21 final size:20
Alignment explanation
Indices: 40905891--40905952 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
40905881 CTTTTGCCTC
* *
40905891 TCTTTTCTTTTTATTTCATTT
1 TCTTTTCTTTTT-TTGCTTTT
*
40905912 TCTTTTTCTTGTTTTGCTTTT
1 TC-TTTTCTTTTTTTGCTTTT
40905933 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTT-TTTGCTTTT
40905953 CTCGTTACAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 12 0.34
21 14 0.40
22 9 0.26
ACGTcount: A:0.03, C:0.15, G:0.05, T:0.77
Consensus pattern (20 bp):
TCTTTTCTTTTTTTGCTTTT
Found at i:40911427 original size:28 final size:28
Alignment explanation
Indices: 40911362--40911462 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
40911352 ATAGTGAATC
*
40911362 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
40911391 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
40911419 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
40911449 CGCACACTTAGTGC
1 CGCACACTTAGTGC
40911463 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:40914005 original size:28 final size:28
Alignment explanation
Indices: 40913972--40914070 Score: 123
Period size: 28 Copynumber: 3.5 Consensus size: 28
40913962 ATGAATAAAT
40913972 GCACTATGTGTGCGAAATTATTAACCGA
1 GCACTATGTGTGCGAAATTATTAACCGA
* * *
40914000 GCACTATGTGTGAGAGATTGGGTGTAA--G-
1 GCACTATGTGTGCGAAATT--AT-TAACCGA
40914028 GCACTATGTGTGCGAAATTATTAACCGA
1 GCACTATGTGTGCGAAATTATTAACCGA
40914056 GCACTATGTGTGCGA
1 GCACTATGTGTGCGA
40914071 GATCGGGTGT
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
25 3 0.05
26 1 0.02
27 1 0.02
28 49 0.83
29 1 0.02
30 1 0.02
31 3 0.05
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.28
Consensus pattern (28 bp):
GCACTATGTGTGCGAAATTATTAACCGA
Found at i:40914036 original size:56 final size:56
Alignment explanation
Indices: 40913972--40914088 Score: 207
Period size: 56 Copynumber: 2.1 Consensus size: 56
40913962 ATGAATAAAT
*
40913972 GCACTATGTGTGCGAAATTATTAACCGAGCACTATGTGTGAGAGATTGGGTGTAAG
1 GCACTATGTGTGCGAAATTATTAACCGAGCACTATGTGTGAGAGATCGGGTGTAAG
* *
40914028 GCACTATGTGTGCGAAATTATTAACCGAGCACTATGTGTGCGAGATCGGGTGTATG
1 GCACTATGTGTGCGAAATTATTAACCGAGCACTATGTGTGAGAGATCGGGTGTAAG
40914084 GCACT
1 GCACT
40914089 GTGTATGTGC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.28
Consensus pattern (56 bp):
GCACTATGTGTGCGAAATTATTAACCGAGCACTATGTGTGAGAGATCGGGTGTAAG
Found at i:40914087 original size:28 final size:27
Alignment explanation
Indices: 40914000--40914088 Score: 74
Period size: 28 Copynumber: 3.2 Consensus size: 27
40913990 TATTAACCGA
*
40914000 GCACTATGTGTGAGAGATTGGGTGTAAG
1 GCACTATGTGTGCGAGA-TGGGTGTAAG
* **
40914028 GCACTATGTGTGCGAAAT-TAT-TAACCG
1 GCACTATGTGTGCGAGATGGGTGTAA--G
*
40914055 AGCACTATGTGTGCGAGATCGGGTGTATG
1 -GCACTATGTGTGCGAGAT-GGGTGTAAG
40914084 GCACT
1 GCACT
40914089 GTGTATGTGC
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
25 3 0.06
26 1 0.02
27 2 0.04
28 37 0.79
29 1 0.02
30 1 0.02
31 2 0.04
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.28
Consensus pattern (27 bp):
GCACTATGTGTGCGAGATGGGTGTAAG
Found at i:40917061 original size:40 final size:40
Alignment explanation
Indices: 40916948--40917119 Score: 161
Period size: 40 Copynumber: 4.2 Consensus size: 40
40916938 TCTTCAGAAT
* * *
40916948 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
* * * *
40916987 TTAACCCGGCCGGGTAT-AGCAACTCGCACAAATGCCTTCGGGTC
1 TT-A---GCCCGGATATAATC-ACTAGCACAAATGCCTTCGGGTC
**
40917031 TTAGCCCGGATATAA-CAACTTTCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAATC-ACTAGCACAAATGCCTTCGGGTC
* * *
40917071 TTAGCCCGGATATAATCACTAGCATAAATGCCATCGGGAC
1 TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
40917111 TTAGCCCGG
1 TTAGCCCGG
40917120 GTATCATTCA
Statistics
Matches: 111, Mismatches: 14, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
39 2 0.02
40 74 0.67
41 2 0.02
43 4 0.04
44 29 0.26
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
Found at i:40925047 original size:40 final size:40
Alignment explanation
Indices: 40924939--40925142 Score: 297
Period size: 40 Copynumber: 5.2 Consensus size: 40
40924929 TCTTCGGAAT
* ** *
40924939 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
* *
40924978 TTAACCCGG-TATAGCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
40925017 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
40925057 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
* * *
40925097 TTAGCCCGGATATAATC-ACTAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGATATAA-CAACTCGCACAAATGCCTTCGGGTC
40925137 TTAGCC
1 TTAGCC
40925143 GGTATCATTC
Statistics
Matches: 151, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
39 36 0.24
40 114 0.75
41 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (40 bp):
TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
Found at i:40933170 original size:40 final size:40
Alignment explanation
Indices: 40933112--40933250 Score: 120
Period size: 40 Copynumber: 3.5 Consensus size: 40
40933102 AAATTGAATG
* *
40933112 ATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATTAT
1 ATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACTAT
* * * ***
40933151 ATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTAT
1 ATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACTAT
* * * ** * *
40933191 ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTATTCT
1 ATCCGGGCTAAGACCCGAAGACAATT-ATGCTAGAAACTAT
40933231 ATCCGGGCTAAGACCCGAAG
1 ATCCGGGCTAAGACCCGAAG
40933251 GCATTTGTGC
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
39 14 0.17
40 70 0.83
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.22
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACTAT
Found at i:40933251 original size:40 final size:39
Alignment explanation
Indices: 40933148--40933276 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 39
40933138 TGCTGGAAAT
* * *
40933148 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGC-ATTGTGCGAGTGAC
* *
40933188 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTAT
1 TATATCCGGGCTAAGACCCGAAGGCATT-GTGCGAGTGAC
* *
40933228 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGAT
1 TATATCCGGGCTAAGACCCGAAGGCA-TTGTGCGA-GTGAC
40933268 TATATCCGG
1 TATATCCGG
40933277 TTATATTCCG
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
39 4 0.05
40 72 0.92
41 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TATATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTGAC
Found at i:40941176 original size:40 final size:40
Alignment explanation
Indices: 40941110--40941276 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
40941100 AAATTGAATG
* * *
40941110 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
40941149 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
40941189 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
40941229 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
40941269 ATATCCGG
1 ATATCCGG
40941277 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:40942998 original size:48 final size:48
Alignment explanation
Indices: 40942852--40943000 Score: 163
Period size: 48 Copynumber: 3.1 Consensus size: 48
40942842 ACATGGTAGG
** * * * * *
40942852 ATGCCAATGCCACATCCCAGATATCGTCTTACATGAGATCACACATCG
1 ATGCCAATGCCATGTCCCAAACATGGTCTTACATGGGATCACACATCA
* * * ** **
40942900 ATACCAATGCTATGTCCCAAACATGGTTTTACATGGGATCGTAGGTCA
1 ATGCCAATGCCATGTCCCAAACATGGTCTTACATGGGATCACACATCA
*
40942948 ATGCCAATGCCATGTCCCAAACATGGTCTTACATGGGATCACATATCA
1 ATGCCAATGCCATGTCCCAAACATGGTCTTACATGGGATCACACATCA
40942996 ATGCC
1 ATGCC
40943001 GATAGCCTAG
Statistics
Matches: 80, Mismatches: 21, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
48 80 1.00
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (48 bp):
ATGCCAATGCCATGTCCCAAACATGGTCTTACATGGGATCACACATCA
Found at i:40948706 original size:30 final size:31
Alignment explanation
Indices: 40948633--40948721 Score: 103
Period size: 30 Copynumber: 3.0 Consensus size: 31
40948623 TTCAATTCAC
* *
40948633 GAGCTAAACCTTAGCTCAACTTCAGCT-TAG
1 GAGCTAAACCTTAGCTCAACTTTAGCTCAAG
* *
40948663 GAGTTTAACCTTAGCTCAACTTTAGCTCAAG
1 GAGCTAAACCTTAGCTCAACTTTAGCTCAAG
* *
40948694 G-GCTAAAGCTTAGCTC-ATTTTAGCTCAA
1 GAGCTAAACCTTAGCTCAACTTTAGCTCAA
40948722 ACCTGATTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
29 11 0.22
30 36 0.72
31 3 0.06
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (31 bp):
GAGCTAAACCTTAGCTCAACTTTAGCTCAAG
Found at i:40951327 original size:5 final size:5
Alignment explanation
Indices: 40951317--40951373 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
40951307 ACGAGAAAAC
*
40951317 AAAGA AAAGA AAAGA AAAGGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAGA AAA-G-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
40951364 AAAGA AAAGA
1 AAAGA AAAGA
40951374 GAGGCAAAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:40951464 original size:12 final size:12
Alignment explanation
Indices: 40951442--40951466 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40951432 TTTGAAAAAC
40951442 AAAAAGAAAATG
1 AAAAAGAAAATG
40951454 AAAAAGAAAATG
1 AAAAAGAAAATG
40951466 A
1 A
40951467 GATTGAAGAA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:40951473 original size:18 final size:18
Alignment explanation
Indices: 40951433--40951486 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
40951423 GAAAAAGCCT
* *
40951433 TTGAAAAACAAAAAGAAA
1 TTGAAAAAGAAAATGAAA
* *
40951451 ATGAAAAAGAAAATGAGA
1 TTGAAAAAGAAAATGAAA
* *
40951469 TTGAAGAAGAGAATGAAA
1 TTGAAAAAGAAAATGAAA
40951487 AAGAGTTTGA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.65, C:0.02, G:0.20, T:0.13
Consensus pattern (18 bp):
TTGAAAAAGAAAATGAAA
Found at i:40951486 original size:24 final size:22
Alignment explanation
Indices: 40951459--40951503 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
40951449 AAATGAAAAA
*
40951459 GAAAATGAGATTGAAGAAGAGAAT
1 GAAAAAGAGATTG-AG-AGAGAAT
*
40951483 GAAAAAGAGTTTGAGAGAGAA
1 GAAAAAGAGATTGAGAGAGAA
40951504 AAAGATTATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 6 0.32
23 2 0.11
24 11 0.58
ACGTcount: A:0.53, C:0.00, G:0.31, T:0.16
Consensus pattern (22 bp):
GAAAAAGAGATTGAGAGAGAAT
Found at i:40953279 original size:30 final size:30
Alignment explanation
Indices: 40953245--40953342 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
40953235 AGCTCACTCC
40953245 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
40953275 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
40953305 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
40953335 TAGCTCAT
1 TAGCTCAT
40953343 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:40954989 original size:13 final size:12
Alignment explanation
Indices: 40954970--40955003 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
40954960 ATACAAGTTT
40954970 GAAAAAAAATTC
1 GAAAAAAAATTC
40954982 GAAAAAAAATTC
1 GAAAAAAAATTC
40954994 GAAAAAAAAT
1 GAAAAAAAAT
40955004 AAAAAGAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.71, C:0.06, G:0.09, T:0.15
Consensus pattern (12 bp):
GAAAAAAAATTC
Found at i:40955940 original size:16 final size:15
Alignment explanation
Indices: 40955921--40955977 Score: 62
Period size: 16 Copynumber: 3.7 Consensus size: 15
40955911 AAGAGAAAAC
40955921 AAAGAAAAGAAAAGAA
1 AAAGAAAAG-AAAGAA
40955937 AAAGCAAAAG-AAGAA
1 AAAG-AAAAGAAAGAA
* *
40955952 AAAGAAAACATAATAA
1 AAAGAAAAGA-AAGAA
40955968 AAAGAAAAGA
1 AAAGAAAAGA
40955978 GAGGCAAGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
14 4 0.11
15 9 0.26
16 17 0.49
17 5 0.14
ACGTcount: A:0.77, C:0.04, G:0.16, T:0.04
Consensus pattern (15 bp):
AAAGAAAAGAAAGAA
Found at i:40955944 original size:21 final size:20
Alignment explanation
Indices: 40955910--40955975 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 20
40955900 ACATTCTTGT
40955910 AAAGAGAAAACAAAGAAAAG-A
1 AAAGA-AAAACAAA-AAAAGAA
*
40955931 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAA-CAAAAAAAGAA
*
40955952 AAAGAAAACATAATAAAAAGAA
1 AAAGAAAA-ACAA-AAAAAGAA
40955974 AA
1 AA
40955976 GAGAGGCAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
20 8 0.21
21 20 0.53
22 10 0.26
ACGTcount: A:0.77, C:0.05, G:0.15, T:0.03
Consensus pattern (20 bp):
AAAGAAAAACAAAAAAAGAA
Found at i:40955952 original size:15 final size:14
Alignment explanation
Indices: 40955921--40955959 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
40955911 AAGAGAAAAC
40955921 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
40955937 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
40955952 AAAGAAAA
1 AAAGAAAA
40955960 CATAATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 4 0.18
15 9 0.41
16 4 0.18
17 5 0.23
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:40956056 original size:11 final size:12
Alignment explanation
Indices: 40956025--40956055 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
40956015 TTGAGAGAAC
40956025 TTGAAAAAGCCT
1 TTGAAAAAGCCT
*
40956037 TTGAAAAAGTCT
1 TTGAAAAAGCCT
40956049 TTGAAAA
1 TTGAAAA
40956056 GCAAAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:40956066 original size:12 final size:12
Alignment explanation
Indices: 40956058--40956082 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40956048 TTTGAAAAGC
40956058 AAAAAGAAAATG
1 AAAAAGAAAATG
40956070 AAAAAGAAAATG
1 AAAAAGAAAATG
40956082 A
1 A
40956083 GATTGAAAAA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:40956079 original size:18 final size:18
Alignment explanation
Indices: 40956052--40956107 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
40956042 AAAGTCTTTG
40956052 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
40956071 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
40956089 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
40956106 AA
1 AA
40956108 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:40956092 original size:30 final size:31
Alignment explanation
Indices: 40956058--40956139 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
40956048 TTTGAAAAGC
*
40956058 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
40956088 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
40956118 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
40956140 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:40958375 original size:30 final size:30
Alignment explanation
Indices: 40958341--40958438 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
40958331 AGCTCACTCC
40958341 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
40958371 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
40958401 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
40958431 TAGCTCAT
1 TAGCTCAT
40958439 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:40960359 original size:26 final size:26
Alignment explanation
Indices: 40960330--40960402 Score: 110
Period size: 26 Copynumber: 2.8 Consensus size: 26
40960320 GAGGAAGTGC
*
40960330 AAAAGGGCTTATGCCCCAGTTTACTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
* * *
40960356 AAAAGGGCGTCTGCCTCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
40960382 AAAAGGGCTTATGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
40960403 ATTAAAAGAG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.25
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:40960665 original size:32 final size:32
Alignment explanation
Indices: 40960624--40960688 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
40960614 CGTTTACAGT
40960624 AAAGGCTTCGGCCCAGTAATATGAAATATGAA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGAA
** *
40960656 AAAGGCTTCGGCCCAGTGTTATGCAATATGAA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGAA
40960688 A
1 A
40960689 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (32 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGAA
Found at i:40963552 original size:34 final size:29
Alignment explanation
Indices: 40963484--40963541 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
40963474 ATTACTCAAA
40963484 AATACAAAACTCATTTTATTAGTTTTGTC
1 AATACAAAACTCATTTTATTAGTTTTGTC
40963513 AATACAAAACTCATTTTATTAGTTTTGTC
1 AATACAAAACTCATTTTATTAGTTTTGTC
40963542 TATCCTATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (29 bp):
AATACAAAACTCATTTTATTAGTTTTGTC
Found at i:40963989 original size:28 final size:27
Alignment explanation
Indices: 40963973--40964102 Score: 129
Period size: 28 Copynumber: 4.7 Consensus size: 27
40963963 CTTACACCCG
*
40963973 ATCTCGCACACATAGTGCTCGGTTAATA
1 ATCTCGCACACATAGTGCTC-GTTAACA
* *
40964001 ATTTCGCACACATAGTGCTCGGTTAATA
1 ATCTCGCACACATAGTGCTC-GTTAACA
*
40964029 ATTTCGCACACATAGTGC-C-TTACACCCA
1 ATCTCGCACACATAGTGCTCGTTA-A--CA
*
40964057 ATCTCGCACACATAGTGCTCGGTTAATA
1 ATCTCGCACACATAGTGCTC-GTTAACA
* *
40964085 ATTTTGCACACATAGTGC
1 ATCTCGCACACATAGTGC
40964103 ATATATTCAT
Statistics
Matches: 90, Mismatches: 6, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
25 3 0.03
26 1 0.01
27 1 0.01
28 80 0.89
29 1 0.01
30 1 0.01
31 3 0.03
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.29
Consensus pattern (27 bp):
ATCTCGCACACATAGTGCTCGTTAACA
Found at i:40964082 original size:84 final size:85
Alignment explanation
Indices: 40963939--40964102 Score: 285
Period size: 84 Copynumber: 1.9 Consensus size: 85
40963929 ATATTCCCTA
*
40963939 AATAATTTCGCACACACACAGTGCCTTACACCCGATCTCGCACACATAGTGCTCGGTTAATAATT
1 AATAATTTCG-ACACACACAGTGCCTTACACCCAATCTCGCACACATAGTGCTCGGTTAATAATT
40964004 TCGCACACATAGTGCTCGGTT
65 TCGCACACATAGTGCTCGGTT
*
40964025 AATAATTTCG-CACACATAGTGCCTTACACCCAATCTCGCACACATAGTGCTCGGTTAATAATTT
1 AATAATTTCGACACACACAGTGCCTTACACCCAATCTCGCACACATAGTGCTCGGTTAATAATTT
*
40964089 TGCACACATAGTGC
66 CGCACACATAGTGC
40964103 ATATATTCAT
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
84 65 0.87
86 10 0.13
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (85 bp):
AATAATTTCGACACACACAGTGCCTTACACCCAATCTCGCACACATAGTGCTCGGTTAATAATTT
CGCACACATAGTGCTCGGTT
Found at i:40977762 original size:71 final size:70
Alignment explanation
Indices: 40977628--40977758 Score: 169
Period size: 71 Copynumber: 1.9 Consensus size: 70
40977618 GCCGATTATG
* * * *
40977628 TTCACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACAT
1 TTCACGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACAT
40977693 TTATCT
65 TTATCT
* *
40977699 TTCACGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 TTCACGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
40977759 TACAGGGTGT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
68 22 0.42
69 1 0.02
70 1 0.02
71 29 0.55
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
TTCACGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATT
TATCT
Found at i:40979594 original size:40 final size:40
Alignment explanation
Indices: 40979549--40979717 Score: 187
Period size: 40 Copynumber: 4.2 Consensus size: 40
40979539 CGGAATATAA
40979549 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
40979589 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
40979629 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * * *
40979669 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
40979709 CCGGATATA
1 CCGGATATA
40979718 TTCAATTTCT
Statistics
Matches: 108, Mismatches: 20, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 1 0.01
40 107 0.99
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:40987577 original size:40 final size:40
Alignment explanation
Indices: 40987532--40987699 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
40987522 CGGAATATAA
40987532 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
40987572 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
40987612 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * * *
40987652 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
40987692 CCGGATAT
1 CCGGATAT
40987700 TATTCAATTT
Statistics
Matches: 107, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 106 0.99
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:40990376 original size:23 final size:23
Alignment explanation
Indices: 40990346--40990390 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
40990336 CACGGCCTAA
40990346 GCACACGGATGCGTATCTTGGCT
1 GCACACGGATGCGTATCTTGGCT
* * *
40990369 GCACACGGGTGTGTGTCTTGGC
1 GCACACGGATGCGTATCTTGGC
40990391 CGTGTGACCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.13, C:0.24, G:0.36, T:0.27
Consensus pattern (23 bp):
GCACACGGATGCGTATCTTGGCT
Found at i:40996023 original size:21 final size:22
Alignment explanation
Indices: 40995998--40996047 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
40995988 TTGTACTTCG
*
40995998 GTACCCCTT-AATTTCATATAC
1 GTACCCCTTAAATTGCATATAC
40996019 GTA-CCCTTAAATTGCATATAC
1 GTACCCCTTAAATTGCATATAC
*
40996040 GTTCCCCT
1 GTACCCCT
40996048 ATTTGTACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 5 0.20
21 16 0.64
22 4 0.16
ACGTcount: A:0.26, C:0.30, G:0.08, T:0.36
Consensus pattern (22 bp):
GTACCCCTTAAATTGCATATAC
Found at i:40996066 original size:41 final size:40
Alignment explanation
Indices: 40996019--40996199 Score: 209
Period size: 41 Copynumber: 4.4 Consensus size: 40
40996009 TTTCATATAC
* * *
40996019 GTACCCTTAAATTGCATATACGTTCCCCTATTTGTACTTTA
1 GTACCCTT-AATTGCACATACGTGCCCCTATTTGTACTTTG
* * * *
40996060 GAACCCTTGAATTACACAAACGTGCCCCTATTTGTACTTCG
1 GTACCCTT-AATTGCACATACGTGCCCCTATTTGTACTTTG
* *
40996101 GTACCCTTCAATTGCATATACGTGCCCCTATTTATACTTTG
1 GTACCCTT-AATTGCACATACGTGCCCCTATTTGTACTTTG
* * *
40996142 GTACCCTTAATTCCACATACGTGCCCCTGTTTGTACTTCG
1 GTACCCTTAATTGCACATACGTGCCCCTATTTGTACTTTG
*
40996182 GTACCATTGAATTGCACA
1 GTACCCTT-AATTGCACA
40996200 GTACCATTGA
Statistics
Matches: 117, Mismatches: 22, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
40 34 0.29
41 83 0.71
ACGTcount: A:0.24, C:0.28, G:0.13, T:0.35
Consensus pattern (40 bp):
GTACCCTTAATTGCACATACGTGCCCCTATTTGTACTTTG
Found at i:40996120 original size:82 final size:81
Alignment explanation
Indices: 40996019--40996197 Score: 259
Period size: 82 Copynumber: 2.2 Consensus size: 81
40996009 TTTCATATAC
* *
40996019 GTACCCTTAAATTGCATATACGTTCCCCTATTTGTACTTTAGAACCCTTGAATTACACAAACGTG
1 GTACCCTTAAATTGCATATACGTGCCCCTATTTATACTTTAGAACCCTT-AATTACACAAACGTG
40996084 CCCCTATTTGTACTTCG
65 CCCCTATTTGTACTTCG
* * * * *
40996101 GTACCCTTCAATTGCATATACGTGCCCCTATTTATACTTTGGTACCCTTAATTCCACATACGTGC
1 GTACCCTTAAATTGCATATACGTGCCCCTATTTATACTTTAGAACCCTTAATTACACAAACGTGC
*
40996166 CCCTGTTTGTACTTCG
66 CCCTATTTGTACTTCG
* *
40996182 GTACCATTGAATTGCA
1 GTACCCTTAAATTGCA
40996198 CAGTACCATT
Statistics
Matches: 87, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
81 43 0.49
82 44 0.51
ACGTcount: A:0.23, C:0.27, G:0.13, T:0.36
Consensus pattern (81 bp):
GTACCCTTAAATTGCATATACGTGCCCCTATTTATACTTTAGAACCCTTAATTACACAAACGTGC
CCCTATTTGTACTTCG
Found at i:40996205 original size:18 final size:18
Alignment explanation
Indices: 40996182--40996217 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
40996172 TTGTACTTCG
40996182 GTACCATTGAATTGCACA
1 GTACCATTGAATTGCACA
40996200 GTACCATTGAATTGCACA
1 GTACCATTGAATTGCACA
40996218 TACATGCCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (18 bp):
GTACCATTGAATTGCACA
Found at i:40996252 original size:59 final size:58
Alignment explanation
Indices: 40996142--40996256 Score: 169
Period size: 59 Copynumber: 2.0 Consensus size: 58
40996132 TTATACTTTG
* * *
40996142 GTACCCTTAATTCCACATACGTGCCCCTGTTTGTACTTCGGTACCATTGAATTGCACA
1 GTACCATTAATTCCACATACATGCCCCTGTTTGTACTTCGGTACCACTGAATTGCACA
*
40996200 GTACCATTGAATTGCACATACATGCCCCTGTTTGTACTTCGGTA-CACCTGAATTGCA
1 GTACCATT-AATTCCACATACATGCCCCTGTTTGTACTTCGGTACCA-CTGAATTGCA
40996257 AATATGTGCC
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
58 9 0.18
59 42 0.82
ACGTcount: A:0.23, C:0.28, G:0.17, T:0.32
Consensus pattern (58 bp):
GTACCATTAATTCCACATACATGCCCCTGTTTGTACTTCGGTACCACTGAATTGCACA
Found at i:40996254 original size:140 final size:141
Alignment explanation
Indices: 40996066--40996321 Score: 354
Period size: 140 Copynumber: 1.8 Consensus size: 141
40996056 TTTAGAACCC
* *
40996066 TTGAATTACACAAACGTGCCCCTATTTGTACTTCGGTACCCTTCAATTGCATATACGTGCCCCTA
1 TTGAATTACACAAACATGCCCCTATTTGTACTTCGGTACCCTTCAATTGCAAATACGTGCCCCTA
* * * *
40996131 TTTATACTTTGGTA-CCCTTAATTCCACATACGTGCCCCTGTTTGTACTTCGGTACCATTGAATT
66 TTTATACTTCGGTACCCCTGAATTCCACATACATGCCCATGTTTGTACTTCGGTACCATTGAATT
40996195 GCACAGTACCA
131 GCACAGTACCA
* * * * *
40996206 TTGAATTGCACATACATGCCCCTGTTTGTACTTCGGTACACC-TGAATTGCAAATATGTGCCCCT
1 TTGAATTACACAAACATGCCCCTATTTGTACTTCGGTAC-CCTTCAATTGCAAATACGTGCCCCT
* * * *
40996270 GTTTGTACTTCGGTACCCCTGAATTGCACATACATTCCCATGTTTGTACTTC
65 ATTTATACTTCGGTACCCCTGAATTCCACATACATGCCCATGTTTGTACTTC
40996322 AATACCCCTA
Statistics
Matches: 99, Mismatches: 15, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
140 66 0.67
141 33 0.33
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (141 bp):
TTGAATTACACAAACATGCCCCTATTTGTACTTCGGTACCCTTCAATTGCAAATACGTGCCCCTA
TTTATACTTCGGTACCCCTGAATTCCACATACATGCCCATGTTTGTACTTCGGTACCATTGAATT
GCACAGTACCA
Found at i:40996267 original size:41 final size:41
Alignment explanation
Indices: 40996207--40996351 Score: 182
Period size: 41 Copynumber: 3.5 Consensus size: 41
40996197 ACAGTACCAT
40996207 TGAATTGCACATACATGCCCCTGTTTGTACTTCGGTACACC
1 TGAATTGCACATACATGCCCCTGTTTGTACTTCGGTACACC
* ** *
40996248 TGAATTGCAAATATGTGCCCCTGTTTGTACTTCGGTACCCC
1 TGAATTGCACATACATGCCCCTGTTTGTACTTCGGTACACC
* * ** *
40996289 TGAATTGCACATACATTCCCATGTTTGTACTTCAATACCCC
1 TGAATTGCACATACATGCCCCTGTTTGTACTTCGGTACACC
* * *
40996330 TAAATTGCATATGCATGCCCCT
1 TGAATTGCACATACATGCCCCT
40996352 ATTTAGACTA
Statistics
Matches: 88, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 88 1.00
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.33
Consensus pattern (41 bp):
TGAATTGCACATACATGCCCCTGTTTGTACTTCGGTACACC
Found at i:40996290 original size:20 final size:20
Alignment explanation
Indices: 40996224--40996290 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
40996214 CACATACATG
40996224 CCCCTGTTTGTACTTCGGTA
1 CCCCTGTTTGTACTTCGGTA
* * * ** ** *
40996244 CACCTGAATTGCAAATATGTG
1 CCCCTG-TTTGTACTTCGGTA
40996265 CCCCTGTTTGTACTTCGGTA
1 CCCCTGTTTGTACTTCGGTA
40996285 CCCCTG
1 CCCCTG
40996291 AATTGCACAT
Statistics
Matches: 30, Mismatches: 16, Indels: 2
0.62 0.33 0.04
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.16, C:0.30, G:0.19, T:0.34
Consensus pattern (20 bp):
CCCCTGTTTGTACTTCGGTA
Found at i:40996293 original size:100 final size:99
Alignment explanation
Indices: 40996101--40996306 Score: 272
Period size: 100 Copynumber: 2.1 Consensus size: 99
40996091 TTGTACTTCG
* * * * * *
40996101 GTACCCTTCAATTGCATATACGTGCCCCTATTTATACTTTGGTACCCTTAATTCCACATACGTGC
1 GTACCATTCAATTGCACATACATGCCCCTATTTATACTTCGGTACCCTGAATTCCAAATACGTGC
*
40996166 CCCTGTTTGTACTTCGGTACCATTGAATTGCACA
66 CCCTGTTTGTACTTCGGTACCACTGAATTGCACA
* * * * *
40996200 GTACCATTGAATTGCACATACATGCCCCTGTTTGTACTTCGGTACACCTGAATTGCAAATATGTG
1 GTACCATTCAATTGCACATACATGCCCCTATTTATACTTCGGTAC-CCTGAATTCCAAATACGTG
*
40996265 CCCCTGTTTGTACTTCGGTACCCCTGAATTGCACA
65 CCCCTGTTTGTACTTCGGTACCACTGAATTGCACA
40996300 -TA-CATTC
1 GTACCATTC
40996307 CCATGTTTGT
Statistics
Matches: 92, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
98 4 0.04
99 40 0.43
100 48 0.52
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.34
Consensus pattern (99 bp):
GTACCATTCAATTGCACATACATGCCCCTATTTATACTTCGGTACCCTGAATTCCAAATACGTGC
CCCTGTTTGTACTTCGGTACCACTGAATTGCACA
Found at i:40999439 original size:68 final size:65
Alignment explanation
Indices: 40999367--40999513 Score: 170
Period size: 64 Copynumber: 2.2 Consensus size: 65
40999357 CATCATGTGT
* * * * *
40999367 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTATGTGTA-CACCAT
1 ACAAGAGAGCTAC-AG-CA-TAT-ATGTAGCTAGGTCGCACGCGTGATACCAAGTGAAGCACCAT
40999431 GTAG
62 GTAG
* * *
40999435 ACAAGAGAGCTACAGGATATATGTAGCTAGGTCGCACGCGTGGTTCCAAGTGAAGGCACCATGTA
1 ACAAGAGAGCTACAGCATATATGTAGCTAGGTCGCACGCGTGATACCAAGTGAA-GCACCATGTA
40999500 G
65 G
40999501 ACAAGAGAGCTAC
1 ACAAGAGAGCTAC
40999514 GAGATAAACT
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
64 27 0.39
65 3 0.04
66 24 0.35
67 2 0.03
68 13 0.19
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (65 bp):
ACAAGAGAGCTACAGCATATATGTAGCTAGGTCGCACGCGTGATACCAAGTGAAGCACCATGTAG
Found at i:41002376 original size:27 final size:27
Alignment explanation
Indices: 41002340--41002391 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
41002330 GTCATACATA
* * *
41002340 TCATAGGGGTATATCAGTCATTTTACC
1 TCATAAGGGTATAACAATCATTTTACC
41002367 TCATAAGGGTATAACAATCATTTTA
1 TCATAAGGGTATAACAATCATTTTA
41002392 TCAAATTGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (27 bp):
TCATAAGGGTATAACAATCATTTTACC
Found at i:41005953 original size:54 final size:53
Alignment explanation
Indices: 41005848--41006001 Score: 134
Period size: 56 Copynumber: 2.8 Consensus size: 53
41005838 CATGACATAG
* * * *
41005848 CACGCCTCTCAACAGGCTACATATGAGCACCCGGACCTAGCATGCATCAC-ATTA
1 CACGACTCTCAACAGGCTACATA--AGCTCCCAGACCTAGCATGCACCACAATTA
* *
41005902 CCACGACTCTCAACAGGGCTACATAAGCTCCCAGACCTAGCGTGTACCACATAATTA
1 -CACGACTCTCAACA-GGCTACATAAGCTCCCAGACCTAGCATGCACCAC--AATTA
* *
41005959 CAC-ACCTCTCAACAAGGCTACACAAGCT-CCTGAACCTAGCATG
1 CACGA-CTCTCAAC-AGGCTACATAAGCTCCCAG-ACCTAGCATG
41006002 TATCATGTCA
Statistics
Matches: 83, Mismatches: 9, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
54 20 0.24
55 17 0.20
56 41 0.49
57 5 0.06
ACGTcount: A:0.31, C:0.35, G:0.16, T:0.18
Consensus pattern (53 bp):
CACGACTCTCAACAGGCTACATAAGCTCCCAGACCTAGCATGCACCACAATTA
Found at i:41011653 original size:25 final size:25
Alignment explanation
Indices: 41011625--41011673 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
41011615 TTATAATATG
* * *
41011625 AAAAATGACTGTTTTGCCCCTAGGT
1 AAAAATGACCGTTATACCCCTAGGT
41011650 AAAAATGACCGTTATACCCCTAGG
1 AAAAATGACCGTTATACCCCTAGG
41011674 GTTTAATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (25 bp):
AAAAATGACCGTTATACCCCTAGGT
Found at i:41011837 original size:24 final size:24
Alignment explanation
Indices: 41011806--41011851 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
41011796 AGGAAGTGAA
**
41011806 AAAGGGCTTTGCC-CCAGTTATTT
1 AAAGGGCTAGGCCTCCAGTTATTT
41011829 AAAGAGGCTAGGCCTCCAGTTAT
1 AAAG-GGCTAGGCCTCCAGTTAT
41011852 ATGATAAAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 7 0.37
25 8 0.42
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (24 bp):
AAAGGGCTAGGCCTCCAGTTATTT
Found at i:41028072 original size:26 final size:27
Alignment explanation
Indices: 41028020--41028078 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
41028010 ACCCATGGAT
* *
41028020 GTATTTCGATATTTTACAAATCGA-GG
1 GTATTTCAATATTTCACAAATCGAGGG
41028046 GTATTTCAATAATTTCACAAATC-AGGG
1 GTATTTCAAT-ATTTCACAAATCGAGGG
41028073 GTATTT
1 GTATTT
41028079 TGGTAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 10 0.34
27 19 0.66
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (27 bp):
GTATTTCAATATTTCACAAATCGAGGG
Found at i:41028085 original size:27 final size:27
Alignment explanation
Indices: 41028030--41028143 Score: 149
Period size: 27 Copynumber: 4.2 Consensus size: 27
41028020 GTATTTCGAT
***
41028030 ATTTTACAAATC-GAGGGTATTTCAATA
1 ATTTTACAAATCAG-GGGTATTTTGGTA
*
41028057 ATTTCACAAATCAGGGGTATTTTGGTA
1 ATTTTACAAATCAGGGGTATTTTGGTA
**
41028084 ATTTTACAAGCCAGGGGTATTTTGGTA
1 ATTTTACAAATCAGGGGTATTTTGGTA
*
41028111 ATTTTACAAATTAGGGGTATTTTGGTA
1 ATTTTACAAATCAGGGGTATTTTGGTA
41028138 ATTTTA
1 ATTTTA
41028144 TTGATTGAGG
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
27 75 0.99
28 1 0.01
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (27 bp):
ATTTTACAAATCAGGGGTATTTTGGTA
Found at i:41028090 original size:54 final size:53
Alignment explanation
Indices: 41028030--41028210 Score: 166
Period size: 54 Copynumber: 3.4 Consensus size: 53
41028020 GTATTTCGAT
*
41028030 ATTTTACAAATCGAGGGTATTTCAATAATTTCACAAATCAGGGGTATTTTGGTA
1 ATTTTACAAATCGAGGGTATTTC-ATAATTTTACAAATCAGGGGTATTTTGGTA
* * ** *
41028084 ATTTTAC-AAGCCAGGGGTATTTTGGTAATTTTACAAATTAGGGGTATTTTGGTA
1 ATTTTACAAATCGA-GGGTA-TTTCATAATTTTACAAATCAGGGGTATTTTGGTA
*** * ** * * *
41028138 ATTTTATTGATTGAGGGTATTTTCATAATTTTGTAAACCAAGGGTATTTTAGTA
1 ATTTTACAAATCGAGGGTA-TTTCATAATTTTACAAATCAGGGGTATTTTGGTA
**
41028192 ATTTTGTAAATCGAGGGTA
1 ATTTTACAAATCGAGGGTA
41028211 AAATGATAAT
Statistics
Matches: 101, Mismatches: 23, Indels: 6
0.78 0.18 0.05
Matches are distributed among these distances:
53 4 0.04
54 92 0.91
55 5 0.05
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.41
Consensus pattern (53 bp):
ATTTTACAAATCGAGGGTATTTCATAATTTTACAAATCAGGGGTATTTTGGTA
Found at i:41028181 original size:27 final size:26
Alignment explanation
Indices: 41028150--41028237 Score: 104
Period size: 27 Copynumber: 3.3 Consensus size: 26
41028140 TTTATTGATT
*
41028150 GAGGGTATTTTCATAATTTTGTAAACC
1 GAGGGTATTTT-ATAATTTTGTAAATC
*
41028177 AAGGGTATTTTAGTAATTTTGTAAATC
1 GAGGGTATTTTA-TAATTTTGTAAATC
** *
41028204 GAGGGTAAAATGATAATTTTGTAAATC
1 GAGGGT-ATTTTATAATTTTGTAAATC
41028231 GAGGGTA
1 GAGGGTA
41028238 AAATGGTAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
26 2 0.04
27 48 0.91
28 3 0.06
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.38
Consensus pattern (26 bp):
GAGGGTATTTTATAATTTTGTAAATC
Found at i:41028220 original size:54 final size:54
Alignment explanation
Indices: 41028162--41028321 Score: 149
Period size: 54 Copynumber: 3.0 Consensus size: 54
41028152 GGGTATTTTC
*** * *
41028162 ATAATTTTGTAAACCAAGGGTATTTTAGTAATTTTGTAAATCGAGGGTAAAATG
1 ATAATTTTGTAAACCAAGGGTAAAATAGTAATTCTGTAAATCAAGGGTAAAATG
* * * *
41028216 ATAATTTTGTAAATCGAGGGTAAAATGGTAATTCTGTAAATCAAGGGTAAAACG
1 ATAATTTTGTAAACCAAGGGTAAAATAGTAATTCTGTAAATCAAGGGTAAAATG
* * * * * ** * **
41028270 GTAATTCTATAAATCGAGGGTAAAACGGTAATTCTATAAATTGAGGGTAAAA
1 ATAATTTTGTAAACCAAGGGTAAAATAGTAATTCTGTAAATCAAGGGTAAAA
41028322 CAATACTTCT
Statistics
Matches: 90, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 90 1.00
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.32
Consensus pattern (54 bp):
ATAATTTTGTAAACCAAGGGTAAAATAGTAATTCTGTAAATCAAGGGTAAAATG
Found at i:41028238 original size:27 final size:27
Alignment explanation
Indices: 41028189--41028322 Score: 187
Period size: 27 Copynumber: 5.0 Consensus size: 27
41028179 GGGTATTTTA
* *
41028189 GTAATTTTGTAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* * *
41028216 ATAATTTTGTAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
41028243 GTAATTCTGTAAATCAAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
41028270 GTAATTCTATAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
41028297 GTAATTCTATAAATTGAGGGTAAAAC
1 GTAATTCTGTAAATCGAGGGTAAAAC
41028323 AATACTTCTA
Statistics
Matches: 99, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 99 1.00
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.30
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAACG
Found at i:41028248 original size:81 final size:81
Alignment explanation
Indices: 41028163--41028321 Score: 192
Period size: 81 Copynumber: 2.0 Consensus size: 81
41028153 GGTATTTTCA
* **** * * * * *
41028163 TAATTTTGTAAACCAAGGGTATTTTAGTAATTTTGTAAATCGAGGGTAAAATGATAATTTTGTAA
1 TAATTCTGTAAACCAAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAACGATAATTCTATAA
41028228 ATCGAGGGTAAAATGG
66 ATCGAGGGTAAAATGG
* * *
41028244 TAATTCTGTAAATCAAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAACGGTAATTCTATAA
1 TAATTCTGTAAACCAAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAACGATAATTCTATAA
*
41028309 ATTGAGGGTAAAA
66 ATCGAGGGTAAAA
41028322 CAATACTTCT
Statistics
Matches: 64, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
81 64 1.00
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.32
Consensus pattern (81 bp):
TAATTCTGTAAACCAAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAACGATAATTCTATAA
ATCGAGGGTAAAATGG
Found at i:41028322 original size:54 final size:54
Alignment explanation
Indices: 41028189--41028344 Score: 204
Period size: 54 Copynumber: 2.9 Consensus size: 54
41028179 GGGTATTTTA
* * * * *
41028189 GTAATTTTGTAAATCGAGGGTAAAATGATAATTTTGTAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACGATAATTCTATAAATCGAGGGTAAAACG
* *
41028243 GTAATTCTGTAAATCAAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACGATAATTCTATAAATCGAGGGTAAAACG
* * * * *
41028297 GTAATTCTATAAATTGAGGGTAAAACAATACTTCTATAAATTGAGGGT
1 GTAATTCTGTAAATCGAGGGTAAAACGATAATTCTATAAATCGAGGGT
41028345 TCTTTGGTAA
Statistics
Matches: 88, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 88 1.00
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.31
Consensus pattern (54 bp):
GTAATTCTGTAAATCGAGGGTAAAACGATAATTCTATAAATCGAGGGTAAAACG
Found at i:41028331 original size:27 final size:27
Alignment explanation
Indices: 41028189--41028344 Score: 168
Period size: 27 Copynumber: 5.8 Consensus size: 27
41028179 GGGTATTTTA
* * * *
41028189 GTAATTTTGTAAATCGAGGGTAAAATG
1 GTAATTCTATAAATTGAGGGTAAAACG
* * * * *
41028216 ATAATTTTGTAAATCGAGGGTAAAATG
1 GTAATTCTATAAATTGAGGGTAAAACG
* **
41028243 GTAATTCTGTAAATCAAGGGTAAAACG
1 GTAATTCTATAAATTGAGGGTAAAACG
*
41028270 GTAATTCTATAAATCGAGGGTAAAACG
1 GTAATTCTATAAATTGAGGGTAAAACG
*
41028297 GTAATTCTATAAATTGAGGGTAAAACA
1 GTAATTCTATAAATTGAGGGTAAAACG
* *
41028324 ATACTTCTATAAATTGAGGGT
1 GTAATTCTATAAATTGAGGGT
41028345 TCTTTGGTAA
Statistics
Matches: 118, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 118 1.00
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.31
Consensus pattern (27 bp):
GTAATTCTATAAATTGAGGGTAAAACG
Found at i:41028344 original size:81 final size:81
Alignment explanation
Indices: 41028189--41028337 Score: 190
Period size: 81 Copynumber: 1.8 Consensus size: 81
41028179 GGGTATTTTA
* * * * * *** *
41028189 GTAATTTTGTAAATCGAGGGTAAAATGATAATTTTGTAAATCGAGGGTAAAATGGTAATTCTGTA
1 GTAATTCTATAAATCGAGGGTAAAACGATAATTCTATAAATCGAGGGTAAAACAATAATTCTATA
41028254 AATCAAGGGTAAAACG
66 AATCAAGGGTAAAACG
* * *
41028270 GTAATTCTATAAATCGAGGGTAAAACGGTAATTCTATAAATTGAGGGTAAAACAATACTTCTATA
1 GTAATTCTATAAATCGAGGGTAAAACGATAATTCTATAAATCGAGGGTAAAACAATAATTCTATA
41028335 AAT
66 AAT
41028338 TGAGGGTTCT
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
81 56 1.00
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.31
Consensus pattern (81 bp):
GTAATTCTATAAATCGAGGGTAAAACGATAATTCTATAAATCGAGGGTAAAACAATAATTCTATA
AATCAAGGGTAAAACG
Found at i:41030575 original size:25 final size:25
Alignment explanation
Indices: 41030547--41030640 Score: 154
Period size: 25 Copynumber: 3.8 Consensus size: 25
41030537 CTCTTTTAAT
* *
41030547 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGGTA
41030572 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGGTA
*
41030597 AACTAGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGGTA
41030622 AACTGGGG-AAAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
41030641 AGCACTTCTT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
24 11 0.17
25 54 0.83
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.26
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGGTA
Found at i:41030577 original size:50 final size:50
Alignment explanation
Indices: 41030534--41030640 Score: 139
Period size: 50 Copynumber: 2.2 Consensus size: 50
41030524 CTGGAGGCCT
* *
41030534 AGCCTCTTTT-AAT-AACTGGGGCAAAGCCCTTTTTGATAAACTGGGGCAA
1 AGCC-CTTTTCAATAAACTAGGGCAAAGCCCTTTTCGATAAACTGGGGCAA
** *
41030583 AGCCCTTTTCGGTAAACTAGGGCAAAGCCCTTTTCGGTAAACTGGGG-AA
1 AGCCCTTTTCAATAAACTAGGGCAAAGCCCTTTTCGATAAACTGGGGCAA
41030632 AGCCCTTTT
1 AGCCCTTTT
41030641 AGCACTTCTT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
48 5 0.10
49 16 0.31
50 30 0.59
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.28
Consensus pattern (50 bp):
AGCCCTTTTCAATAAACTAGGGCAAAGCCCTTTTCGATAAACTGGGGCAA
Done.