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 15 of 318
Found at i:3935734 original size:51 final size:52
Alignment explanation
Indices: 3935654--3935762 Score: 184
Period size: 51 Copynumber: 2.1 Consensus size: 52
3935644 CATGAAATTC
3935654 TTATCATGAAACATTTACCTAACCCATTATCATG-AACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCCA
* * *
3935705 TTATCATGGAACATTTACCTAACCTATTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCCA
3935757 TTATCA
1 TTATCA
3935763 ATTTGTATCA
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
51 32 0.59
52 22 0.41
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.34
Consensus pattern (52 bp):
TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCCA
Found at i:3936278 original size:28 final size:27
Alignment explanation
Indices: 3936227--3936279 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
3936217 TATTATGTAC
*
3936227 ATTTTTAATACTATATATATTGTATGT
1 ATTTTCAATACTATATATATTGTATGT
3936254 ATTTTCAATAACTATAT-TATATGTAT
1 ATTTTCAAT-ACTATATATAT-TGTAT
3936280 ATACTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.53
Consensus pattern (27 bp):
ATTTTCAATACTATATATATTGTATGT
Found at i:3936291 original size:28 final size:28
Alignment explanation
Indices: 3936236--3936291 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
3936226 CATTTTTAAT
* * *
3936236 ACTATATATATTGTATGTATTTTCAATA
1 ACTATATATATTGTATATACTTTAAATA
3936264 ACTATAT-TATATGTATATACTTTAAATA
1 ACTATATATAT-TGTATATACTTTAAATA
3936292 TTATTATGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 3 0.12
28 21 0.88
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.48
Consensus pattern (28 bp):
ACTATATATATTGTATATACTTTAAATA
Found at i:3936314 original size:23 final size:22
Alignment explanation
Indices: 3936267--3936327 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 22
3936257 TTCAATAACT
3936267 ATATTA-TATGTATATACTTTAA
1 ATATTATTATGTA-ATACTTTAA
* *
3936289 ATATTATTATGTAATCATTTTTA
1 ATATTATTATGTAAT-ACTTTAA
3936312 ATATATATATATGTAA
1 ATAT-TAT-TATGTAA
3936328 ATATTTATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
22 8 0.24
23 15 0.45
24 3 0.09
25 7 0.21
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (22 bp):
ATATTATTATGTAATACTTTAA
Found at i:3936333 original size:25 final size:25
Alignment explanation
Indices: 3936100--3936333 Score: 125
Period size: 25 Copynumber: 9.4 Consensus size: 25
3936090 GTTACATTAA
* * *
3936100 GTATATGTTTTTATTATGTATATAT
1 GTATATATTTTTAATATATATATAT
* *
3936125 ATATATATTTTCAATATATAT-TAT
1 GTATATATTTTTAATATATATATAT
* *
3936149 -T-TAGATTATTT-ATATATCATCTTAT
1 GTATATATT-TTTAATATAT-AT-ATAT
* * *
3936174 GTATATATTTTTGATATTATCTCATAC
1 GTATATATTTTTAATA-TATAT-ATAT
3936201 G--TATATTTTTAATA-ACTAT-TAT
1 GTATATATTTTTAATATA-TATATAT
*
3936223 G--TACATTTTTAATACTATATATATT
1 GTATATATTTTTAATA-TATATATA-T
* *
3936248 GTATGTATTTTCAATAACTATATTATAT
1 GTATATATTTTTAAT-A-TATA-TATAT
* *
3936276 GTATATACTTTAAATAT-TAT-TAT
1 GTATATATTTTTAATATATATATAT
3936299 GTA-ATCATTTTTAATATATATATAT
1 GTATAT-ATTTTTAATATATATATAT
*
3936324 GTAAATATTT
1 GTATATATTT
3936334 ATGAAGTATT
Statistics
Matches: 165, Mismatches: 23, Indels: 42
0.72 0.10 0.18
Matches are distributed among these distances:
22 28 0.17
23 24 0.15
24 12 0.07
25 45 0.27
26 7 0.04
27 23 0.14
28 22 0.13
29 4 0.02
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (25 bp):
GTATATATTTTTAATATATATATAT
Found at i:3936365 original size:3 final size:3
Alignment explanation
Indices: 3936359--3936395 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
3936349 TTTTTTTAAA
*
3936359 ATT ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3936396 ATAGTAGTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3937567 original size:4 final size:4
Alignment explanation
Indices: 3937560--3937589 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
3937550 ACACGCAAGC
*
3937560 AAAT AAAT AAAT GAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
3937590 TGGTAGAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:3937687 original size:24 final size:27
Alignment explanation
Indices: 3937628--3937687 Score: 74
Period size: 24 Copynumber: 2.4 Consensus size: 27
3937618 TAATAACGAT
*
3937628 ATGAGTAAAGATAAATGAATAAAATGA
1 ATGAATAAAGATAAATGAATAAAATGA
*
3937655 AT-AAAAAAGA-AAAT-AATAAAAT-A
1 ATGAATAAAGATAAATGAATAAAATGA
3937678 ATGAATAAAG
1 ATGAATAAAG
3937688 CAGGAGATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 3 0.10
24 14 0.48
25 4 0.14
26 6 0.21
27 2 0.07
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.20
Consensus pattern (27 bp):
ATGAATAAAGATAAATGAATAAAATGA
Found at i:3938489 original size:15 final size:15
Alignment explanation
Indices: 3938469--3938503 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
3938459 TCATGTGTAT
3938469 TAATAAGAA-TATTAA
1 TAATAA-AACTATTAA
3938484 TAATAAAACTATTAA
1 TAATAAAACTATTAA
3938499 TAATA
1 TAATA
3938504 TTTTATAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 2 0.11
15 17 0.89
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (15 bp):
TAATAAAACTATTAA
Found at i:3943136 original size:46 final size:46
Alignment explanation
Indices: 3943069--3943250 Score: 235
Period size: 46 Copynumber: 4.0 Consensus size: 46
3943059 AGTGTGCTCT
*
3943069 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATATGTAAGACCATGGTTGAAAGATACCATGGCAAC
3943115 CTGATATGAAATATGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATATGTAAGACCATGGTTGAAAGATACCATGGCAAC
* **
3943161 GTGATATGAAATGA-ACAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAAT-ATGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * *
3943207 ATGACA-GAAA-ATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATGAAATAT--GTAAGACCATGGTTGAAAGATACCATGGCA
3943251 TCATGTCAAA
Statistics
Matches: 121, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
43 1 0.01
45 4 0.03
46 115 0.95
47 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (46 bp):
CTGATATGAAATATGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:3948774 original size:2 final size:2
Alignment explanation
Indices: 3948767--3948792 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3948757 TTTTAATAGT
3948767 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3948793 ACTTAAACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3957657 original size:18 final size:18
Alignment explanation
Indices: 3957645--3957723 Score: 95
Period size: 18 Copynumber: 4.3 Consensus size: 18
3957635 TAACAGTAAG
3957645 TTATTCGGTAACAATCAA
1 TTATTCGGTAACAATCAA
3957663 TTATTCGGTAACAATCAA
1 TTATTCGGTAACAATCAA
** * *
3957681 TTATTCAATAATAATCAG
1 TTATTCGGTAACAATCAA
* *
3957699 TTATTCAGTAACAATTAAA
1 TTATTCGGTAACAA-TCAA
3957718 TTATTC
1 TTATTC
3957724 AATAACAGTC
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
18 44 0.85
19 8 0.15
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.38
Consensus pattern (18 bp):
TTATTCGGTAACAATCAA
Found at i:3957675 original size:36 final size:36
Alignment explanation
Indices: 3957630--3957730 Score: 114
Period size: 36 Copynumber: 2.8 Consensus size: 36
3957620 CGATTATTTT
* **
3957630 TTCAGTAACAGT-AAGTTATTCGGTAACAATCAATTA
1 TTCAGTAACAATCAA-TTATTCAATAACAATCAATTA
* * *
3957666 TTCGGTAACAATCAATTATTCAATAATAATCAGTTA
1 TTCAGTAACAATCAATTATTCAATAACAATCAATTA
*
3957702 TTCAGTAACAATTAAATTATTCAATAACA
1 TTCAGTAACAA-TCAATTATTCAATAACA
3957731 GTCGATCTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
36 37 0.69
37 17 0.31
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.35
Consensus pattern (36 bp):
TTCAGTAACAATCAATTATTCAATAACAATCAATTA
Found at i:3957902 original size:47 final size:47
Alignment explanation
Indices: 3957851--3957954 Score: 163
Period size: 47 Copynumber: 2.2 Consensus size: 47
3957841 CCGAAACAGT
* * *
3957851 AACAGTAGCAATACGGTACACAGAGTACCTCATCTGAACAAATCCGG
1 AACAGTAACAATACGGTACACAGAGTACCTCATCGGAACAAATCCGA
*
3957898 AACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGA
1 AACAGTAACAATACGGTACACAGAGTACCTCATCGGAACAAATCCGA
*
3957945 AACAATAACA
1 AACAGTAACA
3957955 GTAACTGTAA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.42, C:0.25, G:0.17, T:0.15
Consensus pattern (47 bp):
AACAGTAACAATACGGTACACAGAGTACCTCATCGGAACAAATCCGA
Found at i:3957903 original size:53 final size:50
Alignment explanation
Indices: 3957841--3957957 Score: 159
Period size: 47 Copynumber: 2.3 Consensus size: 50
3957831 ATGGCCGAAG
*
3957841 CCGAAACAGTAACAGTAGCAATACGGTACACAGAGTACCTCATCTGAACAAAT
1 CCGAAACAGTAACAGTAG---TACGGTACACAGAGTACCTCATCGGAACAAAT
*
3957894 CCGGAACAGTAAC---AGTACGGTACACAGAGTACCTCATCGGAACAAAT
1 CCGAAACAGTAACAGTAGTACGGTACACAGAGTACCTCATCGGAACAAAT
*
3957941 CCGAAACAATAACAGTA
1 CCGAAACAGTAACAGTA
3957958 ACTGTAACAG
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
47 42 0.74
50 3 0.05
53 12 0.21
ACGTcount: A:0.42, C:0.25, G:0.18, T:0.15
Consensus pattern (50 bp):
CCGAAACAGTAACAGTAGTACGGTACACAGAGTACCTCATCGGAACAAAT
Found at i:3957955 original size:47 final size:47
Alignment explanation
Indices: 3957862--3957957 Score: 165
Period size: 47 Copynumber: 2.0 Consensus size: 47
3957852 ACAGTAGCAA
* * *
3957862 TACGGTACACAGAGTACCTCATCTGAACAAATCCGGAACAGTAACAG
1 TACGGTACACAGAGTACCTCATCGGAACAAATCCGAAACAATAACAG
3957909 TACGGTACACAGAGTACCTCATCGGAACAAATCCGAAACAATAACAG
1 TACGGTACACAGAGTACCTCATCGGAACAAATCCGAAACAATAACAG
3957956 TA
1 TA
3957958 ACTGTAACAG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.41, C:0.25, G:0.18, T:0.17
Consensus pattern (47 bp):
TACGGTACACAGAGTACCTCATCGGAACAAATCCGAAACAATAACAG
Found at i:3958015 original size:12 final size:12
Alignment explanation
Indices: 3957998--3958022 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3957988 TGTGTCGAAT
3957998 CGGTAACAGTAA
1 CGGTAACAGTAA
3958010 CGGTAACAGTAA
1 CGGTAACAGTAA
3958022 C
1 C
3958023 AGTAGTCGGC
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:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTAACAGTAA
Found at i:3959671 original size:2 final size:2
Alignment explanation
Indices: 3959664--3959697 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3959654 TGTTTTACTT
3959664 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3959698 GTTAACTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3959724 original size:15 final size:17
Alignment explanation
Indices: 3959693--3959724 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
3959683 ATATATATAT
3959693 AATATGTTAACTTAATA
1 AATATGTTAACTTAATA
3959710 AATAT-TTAA-TTAATA
1 AATATGTTAACTTAATA
3959725 TCAAATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (17 bp):
AATATGTTAACTTAATA
Found at i:3959829 original size:31 final size:32
Alignment explanation
Indices: 3959773--3959835 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
3959763 CACACTTGTC
*
3959773 ATAATTTAATATATTTATTACATAAAAATCTT
1 ATAATATAATATATTTATTACATAAAAATCTT
*
3959805 ATAATATAA-ATATTTAATTA-ATAAATATCTT
1 ATAATATAATATATTT-ATTACATAAAAATCTT
3959836 TTATAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 16 0.57
32 12 0.43
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (32 bp):
ATAATATAATATATTTATTACATAAAAATCTT
Found at i:3963151 original size:25 final size:25
Alignment explanation
Indices: 3963122--3963169 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
3963112 TTATAATATG
* * *
3963122 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
3963147 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
3963170 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:3963238 original size:20 final size:20
Alignment explanation
Indices: 3963213--3963271 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
3963203 TAAATATGGT
3963213 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
* *
3963233 ATGTATGATACGCACATGAT
1 ATGTATGATATGCACATGAA
3963253 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
3963272 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:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:3963386 original size:22 final size:24
Alignment explanation
Indices: 3963321--3963413 Score: 122
Period size: 23 Copynumber: 4.0 Consensus size: 24
3963311 GAGGAAGTGA
3963321 AAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
3963344 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
3963368 GAAAGGGCTT-TG-CCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
3963390 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
3963414 ATGATAAAGC
Statistics
Matches: 62, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
22 15 0.24
23 28 0.45
24 11 0.18
25 8 0.13
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:3963410 original size:47 final size:47
Alignment explanation
Indices: 3963322--3963413 Score: 127
Period size: 47 Copynumber: 2.0 Consensus size: 47
3963312 AGGAAGTGAA
*
3963322 AAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATTG
1 AAAGGGCTTATGCCCCAGTTATAAAAGGGCTTAGGCCCCAGTTATTG
3963369 AAAGGGCTT-TG-CCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTAGGCC-CCAGTTAT
3963414 ATGATAAAGC
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
45 8 0.20
46 13 0.32
47 20 0.49
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (47 bp):
AAAGGGCTTATGCCCCAGTTATAAAAGGGCTTAGGCCCCAGTTATTG
Found at i:3963656 original size:38 final size:38
Alignment explanation
Indices: 3963605--3963698 Score: 152
Period size: 38 Copynumber: 2.4 Consensus size: 38
3963595 CGTTTACAGT
*
3963605 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACACGA
*
3963643 AAAGGCTTCGGCCCAGTATTATGAAATATGAAATACGA
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACACGA
*
3963681 AAAGGGCTACGGCCCAGT
1 AAA-GGCTTCGGCCCAGT
3963699 GCATGATTGA
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 39 0.75
39 13 0.25
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.21
Consensus pattern (38 bp):
AAAGGCTTCGGCCCAGTATTATGAAATATGAAACACGA
Found at i:3969827 original size:25 final size:25
Alignment explanation
Indices: 3969798--3969845 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
3969788 TTATAATATG
* * *
3969798 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
3969823 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
3969846 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:3969914 original size:20 final size:20
Alignment explanation
Indices: 3969889--3969947 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
3969879 TAAATATGGT
3969889 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
* *
3969909 ATGTATGATACGCACATGAT
1 ATGTATGATATGCACATGAA
3969929 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
3969948 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:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:3970027 original size:23 final size:24
Alignment explanation
Indices: 3969997--3970091 Score: 124
Period size: 24 Copynumber: 4.0 Consensus size: 24
3969987 GAGGAAGTGA
3969997 AAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
3970020 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
3970044 GAAAGGGCTT-TGGCCCCAGTTATT
1 AAAAGGGCTTAT-GCCCCAGTTATT
*
3970068 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
3970092 ATGATAAAGC
Statistics
Matches: 64, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
23 23 0.36
24 30 0.47
25 11 0.17
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:3970065 original size:47 final size:49
Alignment explanation
Indices: 3969998--3970091 Score: 133
Period size: 47 Copynumber: 2.0 Consensus size: 49
3969988 AGGAAGTGAA
*
3969998 AAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTATTG
1 AAAGGGCTTATGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTATTG
3970045 AAAGGGCTT-TGGCCCCAGTTATTAAAAGAGGCTAGGCCTCCAGTTAT
1 AAAGGGCTTAT-GCCCCAGTTATTAAAAGAGGCTAGGCCTCCAGTTAT
3970092 ATGATAAAGC
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
46 1 0.02
47 19 0.45
48 11 0.26
49 11 0.26
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (49 bp):
AAAGGGCTTATGCCCCAGTTATTAAAAGAGGCTAGGCCTCCAGTTATTG
Found at i:3970334 original size:38 final size:38
Alignment explanation
Indices: 3970283--3970376 Score: 152
Period size: 38 Copynumber: 2.4 Consensus size: 38
3970273 CGTTTACAGT
*
3970283 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACACGA
*
3970321 AAAGGCTTCGGCCCAGTATTATGAAATATGAAATACGA
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACACGA
*
3970359 AAAGGGCTACGGCCCAGT
1 AAA-GGCTTCGGCCCAGT
3970377 GCATGATTGA
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 39 0.75
39 13 0.25
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.21
Consensus pattern (38 bp):
AAAGGCTTCGGCCCAGTATTATGAAATATGAAACACGA
Found at i:3974582 original size:26 final size:26
Alignment explanation
Indices: 3974546--3974629 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
3974536 CATGAAATTC
*
3974546 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
3974572 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
3974598 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
3974624 TTATCA
1 TTATCA
3974630 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:3975230 original size:14 final size:14
Alignment explanation
Indices: 3975211--3975250 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
3975201 ATTAAACCAG
* *
3975211 CTTAAACCATATAT
1 CTTAAACCATAAAC
3975225 CTTAAACCATAAAC
1 CTTAAACCATAAAC
*
3975239 CTTAAACTATAA
1 CTTAAACCATAA
3975251 TGATAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (14 bp):
CTTAAACCATAAAC
Found at i:3975464 original size:41 final size:41
Alignment explanation
Indices: 3975407--3975589 Score: 312
Period size: 41 Copynumber: 4.5 Consensus size: 41
3975397 GGGGTTATAG
*
3975407 GGTTTTTAGCGGCGTTTTACCTAAAGCGCCGTTAATGCCCT
1 GGTTTTTAGCGGCGTTTTACCTAAAGCGCCGCTAATGCCCT
*
3975448 GGTTTTTAGCGGCGTTTTACCTAAAGCGCCACTAATGCCCT
1 GGTTTTTAGCGGCGTTTTACCTAAAGCGCCGCTAATGCCCT
* *
3975489 GGTTTTTTGCGGCGTTTTCCCTAAAGCGCCGCTAATGCCCT
1 GGTTTTTAGCGGCGTTTTACCTAAAGCGCCGCTAATGCCCT
*
3975530 GGTTTTTAGCGGCGTTTTCCCTAAAGCGCCGCTAATGCCCT
1 GGTTTTTAGCGGCGTTTTACCTAAAGCGCCGCTAATGCCCT
*
3975571 AGTTTTTAGCGGCGTTTTA
1 GGTTTTTAGCGGCGTTTTA
3975590 GTAAAAAATG
Statistics
Matches: 134, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 134 1.00
ACGTcount: A:0.16, C:0.26, G:0.24, T:0.34
Consensus pattern (41 bp):
GGTTTTTAGCGGCGTTTTACCTAAAGCGCCGCTAATGCCCT
Found at i:3977263 original size:18 final size:18
Alignment explanation
Indices: 3977240--3977325 Score: 102
Period size: 18 Copynumber: 4.7 Consensus size: 18
3977230 GAACGATTAT
*
3977240 TTATTCAGTAACAGTAAG
1 TTATTCAGTAACAATAAG
*
3977258 TTATTCGGTAACAATCAA-
1 TTATTCAGTAACAAT-AAG
* * *
3977276 TTATTCAATAATAATCAG
1 TTATTCAGTAACAATAAG
3977294 TTATTCAGTAACAATTAAG
1 TTATTCAGTAACAA-TAAG
3977313 TTATTCAGTAACA
1 TTATTCAGTAACA
3977326 GTCGATCTTT
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
17 1 0.02
18 37 0.66
19 18 0.32
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (18 bp):
TTATTCAGTAACAATAAG
Found at i:3977281 original size:36 final size:37
Alignment explanation
Indices: 3977240--3977327 Score: 115
Period size: 36 Copynumber: 2.4 Consensus size: 37
3977230 GAACGATTAT
*
3977240 TTATTCAGTAACAGTAAGTTATTCGGTAACAATCAA-
1 TTATTCAGTAACAGTAAGTTATTCAGTAACAATCAAG
* * * * *
3977276 TTATTCAATAATAATCAGTTATTCAGTAACAATTAAG
1 TTATTCAGTAACAGTAAGTTATTCAGTAACAATCAAG
3977313 TTATTCAGTAACAGT
1 TTATTCAGTAACAGT
3977328 CGATCTTTCC
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
36 30 0.71
37 12 0.29
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.36
Consensus pattern (37 bp):
TTATTCAGTAACAGTAAGTTATTCAGTAACAATCAAG
Found at i:3977527 original size:47 final size:47
Alignment explanation
Indices: 3977453--3977559 Score: 162
Period size: 47 Copynumber: 2.3 Consensus size: 47
3977443 CAGTAACAAT
* * * *
3977453 AACAGTAGCAATACGGTACACAGAGTACCTCATCTG-AACAAATCCGG
1 AACAGTAACAGTACGGTACACAAAGTACCTCATC-GAAACAAATCCGA
3977500 AACAGTAACAGTACGGTACACAAAGTACCTCATCGAAACAAATCCGA
1 AACAGTAACAGTACGGTACACAAAGTACCTCATCGAAACAAATCCGA
3977547 AACAGTAACAGTA
1 AACAGTAACAGTA
3977560 ACAGTAACAG
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
46 1 0.02
47 54 0.98
ACGTcount: A:0.43, C:0.24, G:0.17, T:0.16
Consensus pattern (47 bp):
AACAGTAACAGTACGGTACACAAAGTACCTCATCGAAACAAATCCGA
Found at i:3977560 original size:53 final size:52
Alignment explanation
Indices: 3977447--3977565 Score: 142
Period size: 47 Copynumber: 2.4 Consensus size: 52
3977437 CCGAAACAGT
* * * *
3977447 AACAATAACAGTAGCAATACGGTACACAGAGTACCTCATCTGAACAAATCCG
1 AACAGTAACAGTAACAGTACGGTACACAAAGTACCTCATCTGAACAAATCCG
3977499 ----G-AACAGTAACAGTACGGTACACAAAGTACCTCATC-GAAACAAATCCG
1 AACAGTAACAGTAACAGTACGGTACACAAAGTACCTCATCTG-AACAAATCCG
3977546 AAACAGTAACAGTAACAGTA
1 -AACAGTAACAGTAACAGTA
3977566 ACAGAAACAA
Statistics
Matches: 56, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
46 1 0.02
47 41 0.73
52 1 0.02
53 13 0.23
ACGTcount: A:0.45, C:0.24, G:0.16, T:0.16
Consensus pattern (52 bp):
AACAGTAACAGTAACAGTACGGTACACAAAGTACCTCATCTGAACAAATCCG
Found at i:3977564 original size:12 final size:12
Alignment explanation
Indices: 3977545--3977574 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3977535 AAACAAATCC
3977545 GAAACAGTAACA
1 GAAACAGTAACA
*
3977557 GTAACAGTAACA
1 GAAACAGTAACA
3977569 GAAACA
1 GAAACA
3977575 ATATTCGACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.17, G:0.17, T:0.10
Consensus pattern (12 bp):
GAAACAGTAACA
Found at i:3979426 original size:31 final size:32
Alignment explanation
Indices: 3979370--3979432 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
3979360 CACACTTGTC
*
3979370 ATAATTTAATATATTTATTACATAAAAATCTT
1 ATAATATAATATATTTATTACATAAAAATCTT
*
3979402 ATAATATAA-ATATTTAATTA-ATAAATATCTT
1 ATAATATAATATATTT-ATTACATAAAAATCTT
3979433 TTATAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 16 0.57
32 12 0.43
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (32 bp):
ATAATATAATATATTTATTACATAAAAATCTT
Found at i:3989369 original size:33 final size:33
Alignment explanation
Indices: 3989327--3989398 Score: 137
Period size: 33 Copynumber: 2.2 Consensus size: 33
3989317 TACATTCAAG
3989327 GTACC-TAAGCATCATTCAAACCTGCATGACAA
1 GTACCATAAGCATCATTCAAACCTGCATGACAA
3989359 GTACCATAAGCATCATTCAAACCTGCATGACAA
1 GTACCATAAGCATCATTCAAACCTGCATGACAA
3989392 GTACCAT
1 GTACCAT
3989399 TTCAAGATCC
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
32 5 0.13
33 34 0.87
ACGTcount: A:0.38, C:0.28, G:0.12, T:0.22
Consensus pattern (33 bp):
GTACCATAAGCATCATTCAAACCTGCATGACAA
Found at i:3996479 original size:40 final size:40
Alignment explanation
Indices: 3996434--3996510 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
3996424 ACACACCATG
* *
3996434 TGGGGATAAAATCGACCCACCCAGCCCTATACACCAAGTA
1 TGGGGATAAAATCAACCCACCCAGCCCTACACACCAAGTA
*
3996474 TGGGGATAAAATCAACCCATCCAGCCCTACACACCAA
1 TGGGGATAAAATCAACCCACCCAGCCCTACACACCAA
3996511 ATGATACTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.36, C:0.34, G:0.16, T:0.14
Consensus pattern (40 bp):
TGGGGATAAAATCAACCCACCCAGCCCTACACACCAAGTA
Found at i:3996524 original size:40 final size:40
Alignment explanation
Indices: 3996437--3996525 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 40
3996427 CACCATGTGG
* * * **
3996437 GGATAAAATCGACCCACCCAGCCCTATACACCAAGTATGG
1 GGATAAAATCAACCCACCCAGCCCTACACACCAAATATAC
*
3996477 GGATAAAATCAACCCATCCAGCCCTACACACCAAATGATAC
1 GGATAAAATCAACCCACCCAGCCCTACACACCAAAT-ATAC
*
3996518 TG-TAAAAT
1 GGATAAAAT
3996526 AGTACATAAC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
40 38 0.93
41 3 0.07
ACGTcount: A:0.39, C:0.30, G:0.13, T:0.17
Consensus pattern (40 bp):
GGATAAAATCAACCCACCCAGCCCTACACACCAAATATAC
Found at i:4003508 original size:38 final size:39
Alignment explanation
Indices: 4003466--4003557 Score: 98
Period size: 40 Copynumber: 2.4 Consensus size: 39
4003456 ATCTCCGTCG
*
4003466 AACCCAACACACCA-TGTGAGGATAAAATCGACCCA-CT
1 AACCCAACACACCAGTATGAGGATAAAATCGACCCATCT
* * *
4003503 CAACCCTACAAACCAAGTATGGGGATAAAATCGACCCATCT
1 -AACCCAACACACC-AGTATGAGGATAAAATCGACCCATCT
* *
4003544 AGCCCCACACACCA
1 AACCCAACACACCA
4003558 AATGATATTG
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
38 11 0.25
39 2 0.05
40 29 0.66
41 2 0.05
ACGTcount: A:0.39, C:0.35, G:0.13, T:0.13
Consensus pattern (39 bp):
AACCCAACACACCAGTATGAGGATAAAATCGACCCATCT
Found at i:4007272 original size:6 final size:7
Alignment explanation
Indices: 4007251--4007275 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4007241 GACAAAACGT
4007251 AAATAAA
1 AAATAAA
4007258 AAATAAA
1 AAATAAA
4007265 AAATAAA
1 AAATAAA
4007272 AAAT
1 AAAT
4007276 GGACTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
AAATAAA
Found at i:4012040 original size:3 final size:3
Alignment explanation
Indices: 4012032--4012454 Score: 224
Period size: 3 Copynumber: 138.7 Consensus size: 3
4012022 TGAATTTCTG
* * * *
4012032 TAT TAT TAT TAT TAT TAT TGT TACT TAT TAT TAT TAC TGT TAT GTACA
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT -TA-T
* * *
4012080 TAT TAT T-T ATAC TA- TACT TAA TAG TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
4012125 TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
4012172 TAT TA- TAT TAT TAT TAT TAT TA- TATT TAC TAT T-T TATT TAT AAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TA-T TAT TAT
*
4012216 TAT TAAT GTAT TTT TAT TA- TAT ATAT ATAT ATACT CT-T TAT GTAT GGTAT
1 TAT T-AT -TAT TAT TAT TAT TAT -TAT -TAT -TA-T -TAT TAT -TAT --TAT
* * * * *
4012266 T-T TTT TAA CAT TAT TA- TATT TAC TAT TA- TAT TAT TAT CT-T TAA
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT -TAT TAT
** *
4012309 TA- TAT TA- TAT T-T TACT T-T CCT CACCT TAT TAT TAT GTCA- TACT
1 TAT TAT TAT TAT TAT TA-T TAT TAT TA--T TAT TAT TAT -T-AT TA-T
* **
4012352 T-T CT-T TGT T-T T-T TGC TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4012394 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT TA- TATT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TA-T
*
4012440 TAT ATAA TAT TAT TA
1 TAT -TAT TAT TAT TA
4012455 ATAGGTACTT
Statistics
Matches: 338, Mismatches: 37, Indels: 90
0.73 0.08 0.19
Matches are distributed among these distances:
2 37 0.11
3 246 0.73
4 45 0.13
5 10 0.03
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:4012602 original size:19 final size:20
Alignment explanation
Indices: 4012545--4012603 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
4012535 AACGCCATAT
* * *
4012545 TATGTACATATTTTTAATGC
1 TATGTATATACTTTTAATAC
* *
4012565 TATGTGTACACTTTGTAATAC
1 TATGTATATACTTT-TAATAC
4012586 TATGTATATA-TTTTAATA
1 TATGTATATACTTTTAATA
4012604 TCATTAGTTA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
19 5 0.16
20 13 0.42
21 13 0.42
ACGTcount: A:0.32, C:0.08, G:0.10, T:0.49
Consensus pattern (20 bp):
TATGTATATACTTTTAATAC
Found at i:4012889 original size:22 final size:23
Alignment explanation
Indices: 4012840--4012889 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
4012830 GTATTAATCT
*
4012840 TAGTACATATATATTTTATTATA
1 TAGTATATATATATTTTATTATA
*
4012863 -CGTATATATATATTTT-TTATA
1 TAGTATATATATATTTTATTATA
4012884 TAGTAT
1 TAGTAT
4012890 TATTTTCGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.54
Consensus pattern (23 bp):
TAGTATATATATATTTTATTATA
Found at i:4012969 original size:3 final size:3
Alignment explanation
Indices: 4012961--4013034 Score: 141
Period size: 3 Copynumber: 25.0 Consensus size: 3
4012951 CGTACATACT
4012961 TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4013008 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
4013035 GTATATAAAT
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 68 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:4016002 original size:59 final size:60
Alignment explanation
Indices: 4015928--4016048 Score: 219
Period size: 59 Copynumber: 2.0 Consensus size: 60
4015918 TAAACAGTGG
4015928 TTGAACTCATTGCCATGAGGGTCAATCACTACTTGGGAACAAATGACCG-AAAAATTTCTA
1 TTGAACTCATTGCCATGAGGGTCAATCACTACTT-GGAACAAATGACCGAAAAAATTTCTA
4015988 TTGAACT-ATTGCCATGAGGGTCAATCACTACTTGGAACAAATGACCGAAAAAATTTCTA
1 TTGAACTCATTGCCATGAGGGTCAATCACTACTTGGAACAAATGACCGAAAAAATTTCTA
4016047 TT
1 TT
4016049 AAAATATTTC
Statistics
Matches: 60, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
58 14 0.23
59 39 0.65
60 7 0.12
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (60 bp):
TTGAACTCATTGCCATGAGGGTCAATCACTACTTGGAACAAATGACCGAAAAAATTTCTA
Found at i:4024234 original size:3 final size:3
Alignment explanation
Indices: 4024228--4024276 Score: 75
Period size: 3 Copynumber: 16.7 Consensus size: 3
4024218 GCATAAAAGA
4024228 AAT AAT AGA- AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4024272 AAT AA
1 AAT AA
4024277 AGAAACAGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 3 0.07
3 39 0.91
4 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:4028405 original size:20 final size:20
Alignment explanation
Indices: 4028380--4028439 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 20
4028370 ATAAGTTAGT
4028380 TCAAGTGGTAAATCCTAAAG
1 TCAAGTGGTAAATCCTAAAG
4028400 TCAAGT-G---AT--T--AG
1 TCAAGTGGTAAATCCTAAAG
4028412 TTCAAGTGGTAAATCCTAAAG
1 -TCAAGTGGTAAATCCTAAAG
4028433 TCAAGTG
1 TCAAGTG
4028440 ATTTTAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 18
0.63 0.00 0.37
Matches are distributed among these distances:
12 2 0.06
13 6 0.19
14 2 0.06
16 2 0.06
17 2 0.06
19 2 0.06
20 13 0.42
21 2 0.06
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (20 bp):
TCAAGTGGTAAATCCTAAAG
Found at i:4028417 original size:33 final size:33
Alignment explanation
Indices: 4028375--4028442 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
4028365 AACGAATAAG
4028375 TTAGTTCAAGTGGTAAATCCTAAAGTCAAGTGA
1 TTAGTTCAAGTGGTAAATCCTAAAGTCAAGTGA
4028408 TTAGTTCAAGTGGTAAATCCTAAAGTCAAGTGA
1 TTAGTTCAAGTGGTAAATCCTAAAGTCAAGTGA
4028441 TT
1 TT
4028443 TTAAAAAAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (33 bp):
TTAGTTCAAGTGGTAAATCCTAAAGTCAAGTGA
Found at i:4031904 original size:2 final size:2
Alignment explanation
Indices: 4031897--4031930 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4031887 AAGCCAATTC
4031897 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4031931 TACTCATCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4033733 original size:41 final size:41
Alignment explanation
Indices: 4033392--4033732 Score: 506
Period size: 41 Copynumber: 8.3 Consensus size: 41
4033382 ATAAAATTTT
* *
4033392 CTAGGC-ATAAAGCCT-AGTATAATACACCGGCACAGAGCCTA
1 CTAGGCAAT-AAGCCTGA-TATAATACACCGGCACAAAGCCTG
* *
4033433 CTAGGCAATAAGCCTGATATAATACACCGGCATATAAAGCCTA
1 CTAGGCAATAAGCCTGATATAATACACCGGC--ACAAAGCCTG
*
4033476 CTAGGCAATAAGCTTGATATAATACACCGGCACAAAGCCTG
1 CTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCCTG
* *
4033517 CTAGGCAATAAGCCTGATTTAATACACCGGCACAAAGCTTG
1 CTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCCTG
*
4033558 CTAGGCAATAAGCCTGATTTAATACACCGGCACAAAGCCTG
1 CTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCCTG
* * *
4033599 CTAGGCAATAAGCCTGATTTAAAACACTGGCACAAAGCCTG
1 CTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCCTG
*
4033640 CTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCATG
1 CTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCCTG
* *
4033681 CTAGGCAATAAACATGATATAATACACCGGCACAAAGCCTG
1 CTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCCTG
4033722 CTAGGCAATAA
1 CTAGGCAATAA
4033733 AGCCCAAATA
Statistics
Matches: 278, Mismatches: 18, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
41 237 0.85
42 3 0.01
43 38 0.14
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (41 bp):
CTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCCTG
Found at i:4036265 original size:11 final size:11
Alignment explanation
Indices: 4036251--4036306 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
4036241 AGATAAATAT
4036251 TATTTTATTAA
1 TATTTTATTAA
*
4036262 TATTTTAATAAGA
1 TATTTT-ATTA-A
* *
4036275 TATTTTACTAT
1 TATTTTATTAA
*
4036286 TATTTTATTAT
1 TATTTTATTAA
4036297 TATTTTATTA
1 TATTTTATTA
4036307 GTATATAAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
11 26 0.68
12 5 0.13
13 7 0.18
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:4038478 original size:46 final size:46
Alignment explanation
Indices: 4038431--4038699 Score: 369
Period size: 46 Copynumber: 5.8 Consensus size: 46
4038421 GCTCTCTGAT
** * *
4038431 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
** * *
4038477 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAATGTGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
4038523 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
*
4038569 ATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
* * *
4038615 ATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCGACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
* * * * *
4038661 A-GAAAATGAGTAAAACCATAGTTGAAAGACACTATGGCA
1 ATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCA
4038700 TCATGTCAAA
Statistics
Matches: 206, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
45 1 0.00
46 205 1.00
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (46 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
Found at i:4039978 original size:20 final size:18
Alignment explanation
Indices: 4039944--4039983 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 18
4039934 TTATGAAAAA
4039944 TTTTCTAAATTTTCTAAG
1 TTTTCTAAATTTTCTAAG
4039962 TTTTCTAAAAGTTTTCTAAG
1 TTTTCT-AAA-TTTTCTAAG
4039982 TT
1 TT
4039984 ATCGATTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 6 0.30
19 3 0.15
20 11 0.55
ACGTcount: A:0.28, C:0.10, G:0.07, T:0.55
Consensus pattern (18 bp):
TTTTCTAAATTTTCTAAG
Found at i:4039982 original size:9 final size:9
Alignment explanation
Indices: 4039944--4039983 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
4039934 TTATGAAAAA
*
4039944 TTTTCTAAA
1 TTTTCTAAG
4039953 TTTTCTAAG
1 TTTTCTAAG
4039962 TTTTCTAAAAG
1 TTTTCT--AAG
4039973 TTTTCTAAG
1 TTTTCTAAG
4039982 TT
1 TT
4039984 ATCGATTTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 19 0.68
11 9 0.32
ACGTcount: A:0.28, C:0.10, G:0.07, T:0.55
Consensus pattern (9 bp):
TTTTCTAAG
Found at i:4042345 original size:24 final size:23
Alignment explanation
Indices: 4042317--4042362 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
4042307 ATCTTAAAGT
*
4042317 TGTTAGAATTAATTATCAGGTGGC
1 TGTTAGAATTAATT-TCAAGTGGC
*
4042341 TGTTAGCATTAATTTCAAGTGG
1 TGTTAGAATTAATTTCAAGTGG
4042363 TGTGCATGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.28, C:0.09, G:0.24, T:0.39
Consensus pattern (23 bp):
TGTTAGAATTAATTTCAAGTGGC
Found at i:4044451 original size:47 final size:47
Alignment explanation
Indices: 4044382--4044475 Score: 154
Period size: 47 Copynumber: 2.0 Consensus size: 47
4044372 AAACATTTTT
* *
4044382 TGTTTTAGGAACTAATTTAAAATTTTAA-TGATAATTTGAGGTTGTCA
1 TGTTTTAGGAACTAATTTAAAATTTTAACT-ATAAATTGAGATTGTCA
4044429 TGTTTTAGGAACTAATTTAAAATTTTAACTATAAATTGAGATTGTCA
1 TGTTTTAGGAACTAATTTAAAATTTTAACTATAAATTGAGATTGTCA
4044476 AGTGGAATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
47 43 0.98
48 1 0.02
ACGTcount: A:0.36, C:0.05, G:0.15, T:0.44
Consensus pattern (47 bp):
TGTTTTAGGAACTAATTTAAAATTTTAACTATAAATTGAGATTGTCA
Found at i:4047326 original size:21 final size:20
Alignment explanation
Indices: 4047277--4047330 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
4047267 CCCTCAAAAA
**
4047277 TTTTGAAAATTTTAATTTGAC
1 TTTT-AAAATTTTAATTAAAC
*
4047298 TTTGAAAATTTTAATTAAACC
1 TTTTAAAATTTTAATTAAA-C
4047319 TTTTAAAATTTT
1 TTTTAAAATTTT
4047331 TGAAAATTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTAAAATTTTAATTAAAC
Found at i:4052893 original size:36 final size:36
Alignment explanation
Indices: 4052851--4052919 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
4052841 TTGCTTGTCT
4052851 TCAAACAAAATCCCCAACCCACATGCAAGTTAATCC
1 TCAAACAAAATCCCCAACCCACATGCAAGTTAATCC
4052887 TCAAACAAAATCCCCAACCCACATGCAAGTTAA
1 TCAAACAAAATCCCCAACCCACATGCAAGTTAA
4052920 CTTTTCTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.43, C:0.35, G:0.06, T:0.16
Consensus pattern (36 bp):
TCAAACAAAATCCCCAACCCACATGCAAGTTAATCC
Found at i:4053588 original size:70 final size:70
Alignment explanation
Indices: 4053514--4053655 Score: 266
Period size: 70 Copynumber: 2.0 Consensus size: 70
4053504 TTTTATTTTG
* *
4053514 ATTTTTTATTGATTTTTTTAAATAAAATTCAGCAATTCAAATAATGGAACATAGTTAGGTAACTA
1 ATTTTTTATTGATTTTTTTAAATAAAATTCAACAATTCAAATAATGGAACATAGTTAGGCAACTA
4053579 ACCAA
66 ACCAA
4053584 ATTTTTTATTGATTTTTTTAAATAAAATTCAACAATTCAAATAATGGAACATAGTTAGGCAACTA
1 ATTTTTTATTGATTTTTTTAAATAAAATTCAACAATTCAAATAATGGAACATAGTTAGGCAACTA
4053649 ACCAA
66 ACCAA
4053654 AT
1 AT
4053656 CAAATCTCAA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (70 bp):
ATTTTTTATTGATTTTTTTAAATAAAATTCAACAATTCAAATAATGGAACATAGTTAGGCAACTA
ACCAA
Found at i:4058324 original size:43 final size:43
Alignment explanation
Indices: 4058258--4058386 Score: 183
Period size: 44 Copynumber: 3.0 Consensus size: 43
4058248 AGCTCGAACA
4058258 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCG
* *
4058301 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGTAAATCACAAATCG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACATGT-AATCACATATCG
*
4058345 ATGCCAACGTCCCAAACGTGGTCTTACATG-AATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCG
4058387 GAATCCTATG
Statistics
Matches: 76, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
42 13 0.17
43 26 0.34
44 35 0.46
45 2 0.03
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCG
Found at i:4058707 original size:9 final size:9
Alignment explanation
Indices: 4058668--4058735 Score: 82
Period size: 9 Copynumber: 7.6 Consensus size: 9
4058658 ATAAGTATAA
4058668 AATTAACCG
1 AATTAACCG
* *
4058677 AATTTACTG
1 AATTAACCG
* *
4058686 AATTAATCA
1 AATTAACCG
4058695 AATTAACCG
1 AATTAACCG
* *
4058704 AATTACCCA
1 AATTAACCG
4058713 AATTAACCG
1 AATTAACCG
4058722 AATTAACCG
1 AATTAACCG
4058731 AATTA
1 AATTA
4058736 TTTGTATAAA
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 47 1.00
ACGTcount: A:0.46, C:0.19, G:0.07, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:4058783 original size:14 final size:14
Alignment explanation
Indices: 4058766--4058806 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
4058756 TTTTATTTTT
4058766 ATTTTTAGTTTTAG
1 ATTTTTAGTTTTAG
*
4058780 ATTTTTAGTATTAG
1 ATTTTTAGTTTTAG
*
4058794 ATTTTTATTTTTA
1 ATTTTTAGTTTTA
4058807 TTTATTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.66
Consensus pattern (14 bp):
ATTTTTAGTTTTAG
Found at i:4058798 original size:21 final size:20
Alignment explanation
Indices: 4058755--4058829 Score: 71
Period size: 20 Copynumber: 3.6 Consensus size: 20
4058745 AATTATATGT
* *
4058755 TTTTTATTTTTATTTTTAG-
1 TTTTAATTTTTATTATTAGA
*
4058774 TTTTAGATTTTTAGTATTAGA
1 TTTTA-ATTTTTATTATTAGA
* *
4058795 TTTTTATTTTTATTTATTAAA
1 TTTTAATTTTTA-TTATTAGA
4058816 TTTGTAATTTTTAT
1 TTT-TAATTTTTAT
4058830 GATTGGGTTG
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
19 4 0.09
20 19 0.42
21 14 0.31
22 8 0.18
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (20 bp):
TTTTAATTTTTATTATTAGA
Found at i:4060175 original size:13 final size:13
Alignment explanation
Indices: 4060157--4060181 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4060147 TCAAACGATA
4060157 AAATTTTCACACG
1 AAATTTTCACACG
4060170 AAATTTTCACAC
1 AAATTTTCACAC
4060182 ATATAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:4061220 original size:16 final size:17
Alignment explanation
Indices: 4061201--4061241 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
4061191 TGTTAGTTAT
4061201 ATAAATTTAATT-TAAA
1 ATAAATTTAATTATAAA
*
4061217 ATAACTTTAATTATAAA
1 ATAAATTTAATTATAAA
4061234 ATCAAATT
1 AT-AAATT
4061242 GTAAATCCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 11 0.52
17 6 0.29
18 4 0.19
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAAATTTAATTATAAA
Found at i:4063933 original size:18 final size:16
Alignment explanation
Indices: 4063894--4063934 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 16
4063884 TGCCTATTTT
*
4063894 GTTTCAAAACCTAGAG
1 GTTTCAAAACCTAGAC
4063910 GTTTCAAAACCTGAGAAC
1 GTTTCAAAACCT-AG-AC
4063928 GTTTCAA
1 GTTTCAA
4063935 CAATGGGGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 12 0.55
17 2 0.09
18 8 0.36
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.27
Consensus pattern (16 bp):
GTTTCAAAACCTAGAC
Found at i:4064825 original size:30 final size:31
Alignment explanation
Indices: 4064791--4064857 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
4064781 TTACAAAATG
4064791 GTCATTAAACTATTCAAAAG-TTATTTTTAA
1 GTCATTAAACTATTCAAAAGTTTATTTTTAA
* ** * *
4064821 GTCATTGAACTATTTGAAAGTTTTTTTTTGA
1 GTCATTAAACTATTCAAAAGTTTATTTTTAA
4064852 GTCATT
1 GTCATT
4064858 TGGATGTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 17 0.55
31 14 0.45
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (31 bp):
GTCATTAAACTATTCAAAAGTTTATTTTTAA
Found at i:4066460 original size:18 final size:19
Alignment explanation
Indices: 4066434--4066469 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
4066424 AAAGTCGTTA
4066434 AATTCAACCCAA-AATAAT
1 AATTCAACCCAATAATAAT
*
4066452 AATTTAACCCAATAATAA
1 AATTCAACCCAATAATAA
4066470 CTATTGTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.56, C:0.19, G:0.00, T:0.25
Consensus pattern (19 bp):
AATTCAACCCAATAATAAT
Found at i:4070085 original size:18 final size:18
Alignment explanation
Indices: 4070064--4070103 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
4070054 AAAACATTTC
*
4070064 AAAAATAGA-AAAACCACA
1 AAAAATAAAGAAAACC-CA
4070082 AAAAATAAAGAAAACCCA
1 AAAAATAAAGAAAACCCA
4070100 AAAA
1 AAAA
4070104 CTTAGAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.75, C:0.15, G:0.05, T:0.05
Consensus pattern (18 bp):
AAAAATAAAGAAAACCCA
Found at i:4070369 original size:30 final size:30
Alignment explanation
Indices: 4070325--4070384 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
4070315 CACGGGCTGG
*
4070325 CACATGGGCATGTGGCCTACCCGTGTGGAT
1 CACATAGGCATGTGGCCTACCCGTGTGGAT
* *
4070355 CACATAGGCGTGTGGCCTGCCCGTGTGGAT
1 CACATAGGCATGTGGCCTACCCGTGTGGAT
4070385 ATTGAAAACT
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:0.15, C:0.27, G:0.35, T:0.23
Consensus pattern (30 bp):
CACATAGGCATGTGGCCTACCCGTGTGGAT
Found at i:4071849 original size:27 final size:28
Alignment explanation
Indices: 4071818--4071877 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 28
4071808 TATTCATTAT
4071818 TTTAACATTACTTTTTT-AAAATTGTAG
1 TTTAACATTACTTTTTTGAAAATTGTAG
* ** **
4071845 TTTAAGATTTTTTTTTTGAAGGTTGTAG
1 TTTAACATTACTTTTTTGAAAATTGTAG
4071873 TTTAA
1 TTTAA
4071878 GTTTTTAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 14 0.52
28 13 0.48
ACGTcount: A:0.28, C:0.03, G:0.13, T:0.55
Consensus pattern (28 bp):
TTTAACATTACTTTTTTGAAAATTGTAG
Found at i:4073442 original size:23 final size:24
Alignment explanation
Indices: 4073394--4073445 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
4073384 ATTTAAATAT
4073394 AAAAT-ATTTAATTTTATATTATA
1 AAAATAATTTAATTTTATATTATA
*
4073417 AAAATAATTATAATTTT-TTTTA-A
1 AAAATAATT-TAATTTTATATTATA
4073440 AAAATA
1 AAAATA
4073446 CAGTTTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 12 0.46
24 7 0.27
25 7 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATAATTTAATTTTATATTATA
Found at i:4075500 original size:15 final size:16
Alignment explanation
Indices: 4075467--4075514 Score: 55
Period size: 15 Copynumber: 3.0 Consensus size: 16
4075457 CTGACCATAA
4075467 TTTAAATATATATTTT
1 TTTAAATATATATTTT
4075483 TTTAAATAT-TCA-TTT
1 TTTAAATATAT-ATTTT
*
4075498 TTTAAATTTAATATTTT
1 TTTAAATAT-ATATTTT
4075515 ATCTAAAACC
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
15 12 0.44
16 11 0.41
17 4 0.15
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTAAATATATATTTT
Found at i:4076055 original size:3 final size:3
Alignment explanation
Indices: 4076047--4076114 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
4076037 AAGCCCCTGT
4076047 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
4076095 TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TT
4076115 TTGCACTCAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:4076711 original size:28 final size:29
Alignment explanation
Indices: 4076680--4076734 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
4076670 AGTAAAATCA
*
4076680 ATAAAAATTATT-ATATTTTAATAAAAAT
1 ATAAAAATTATTAAAATTTTAATAAAAAT
***
4076708 ATAAGTTTTATTAAAATTTTAATAAAA
1 ATAAAAATTATTAAAATTTTAATAAAA
4076735 TTGTACAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 9 0.41
29 13 0.59
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (29 bp):
ATAAAAATTATTAAAATTTTAATAAAAAT
Found at i:4076773 original size:29 final size:29
Alignment explanation
Indices: 4076729--4076849 Score: 106
Period size: 29 Copynumber: 4.2 Consensus size: 29
4076719 TAAAATTTTA
* * *
4076729 ATAAAATTGTACAAAAGTTATAAAAAATT
1 ATAAAATTTTATAAAAGTCATAAAAAATT
* * *
4076758 GTAAAATTTTATAAAAATCGTAAAAAA-T
1 ATAAAATTTTATAAAAGTCATAAAAAATT
* *
4076786 ATAAAA-TATATAGAAATGT-AGAAAAAATT
1 ATAAAATTTTATA-AAA-GTCATAAAAAATT
4076815 ATAAAATTTTAT-AAAGTCATAAGAAAATT
1 ATAAAATTTTATAAAAGTCATAA-AAAATT
*
4076844 AGAAAA
1 ATAAAA
4076850 AATGAAAAGA
Statistics
Matches: 72, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
27 7 0.10
28 21 0.29
29 40 0.56
30 4 0.06
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.30
Consensus pattern (29 bp):
ATAAAATTTTATAAAAGTCATAAAAAATT
Found at i:4076775 original size:19 final size:19
Alignment explanation
Indices: 4076719--4076782 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
4076709 TAAGTTTTAT
4076719 TAAAATTTTA-ATAAAATTG
1 TAAAATTTTATA-AAAATTG
**
4076738 TACAAAAGTTATAAAAAATTG
1 TA-AAATTTTAT-AAAAATTG
*
4076759 TAAAATTTTATAAAAATCG
1 TAAAATTTTATAAAAATTG
4076778 TAAAA
1 TAAAA
4076783 AATATAAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
19 14 0.38
20 13 0.35
21 9 0.24
22 1 0.03
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.34
Consensus pattern (19 bp):
TAAAATTTTATAAAAATTG
Found at i:4076887 original size:9 final size:10
Alignment explanation
Indices: 4076720--4076887 Score: 57
Period size: 10 Copynumber: 17.2 Consensus size: 10
4076710 AAGTTTTATT
*
4076720 AAAATTTTAA
1 AAAATTATAA
*
4076730 TAAAATTGTACA
1 -AAAATTATA-A
*
4076742 AAAGTTATAA
1 AAAATTATAA
*
4076752 AAAATTGTAA
1 AAAATTATAA
**
4076762 AATTTTAT-A
1 AAAATTATAA
**
4076771 AAAATCGTAA
1 AAAATTATAA
4076781 AAAA-TATAA
1 AAAATTATAA
*
4076790 AATA-TAT-A
1 AAAATTATAA
* *
4076798 GAAATGTAGAA
1 AAAAT-TATAA
4076809 AAAATTAT--
1 AAAATTATAA
* *
4076817 AAAATTTTAT
1 AAAATTATAA
* *
4076827 AAAGTCATAA
1 AAAATTATAA
*
4076837 GAAAATTAGAA
1 -AAAATTATAA
*
4076848 AAAATGA-AA
1 AAAATTATAA
* *
4076857 AGAA--ATAC
1 AAAATTATAA
4076865 AAAATTCATAA
1 AAAATT-ATAA
4076876 AAAATTATAA
1 AAAATTATAA
4076886 AA
1 AA
4076888 CTTATCATAC
Statistics
Matches: 112, Mismatches: 33, Indels: 25
0.66 0.19 0.15
Matches are distributed among these distances:
7 1 0.01
8 14 0.12
9 19 0.17
10 41 0.37
11 36 0.32
12 1 0.01
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.29
Consensus pattern (10 bp):
AAAATTATAA
Found at i:4078667 original size:32 final size:32
Alignment explanation
Indices: 4078629--4078689 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
4078619 TTATAAATTT
*
4078629 ATAAATTGATTACTTGAATTTAATAACTCATA
1 ATAAATTAATTACTTGAATTTAATAACTCATA
* *
4078661 ATAAATTAATTAGTTTAATTTAATAACTC
1 ATAAATTAATTACTTGAATTTAATAACTC
4078690 GTCCCGATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.43
Consensus pattern (32 bp):
ATAAATTAATTACTTGAATTTAATAACTCATA
Found at i:4081538 original size:42 final size:42
Alignment explanation
Indices: 4081426--4081547 Score: 156
Period size: 43 Copynumber: 2.9 Consensus size: 42
4081416 TACCAAACTA
* *
4081426 ATGCCATATCCCAAATATGGTCTTACATGTAATCTCGTATCG
1 ATGCCATATCCCAAATATGGTCTTACACGTAATCTCATATCG
* * **
4081468 ATACCAATAGCCCAGCTATGGTCTTACACG-AAGTCTCATATCG
1 ATGCC-ATATCCCAAATATGGTCTTACACGTAA-TCTCATATCG
*
4081511 ATGCCATATCCCATATATGGTCTTACACGTAATCTCA
1 ATGCCATATCCCAAATATGGTCTTACACGTAATCTCA
4081548 GTAACCTTAA
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
42 32 0.48
43 35 0.52
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAAATATGGTCTTACACGTAATCTCATATCG
Found at i:4085471 original size:36 final size:34
Alignment explanation
Indices: 4085416--4085512 Score: 97
Period size: 36 Copynumber: 2.8 Consensus size: 34
4085406 TTATTGATTT
* * *
4085416 ATAAATAAATTTATATTTTATAATAAGTAAA-TTAA
1 ATAAAAAAATATAAATTTTATAATAA-TAAACTT-A
*
4085451 ATAAAAATAATATAAATTTTATAATATATAAACTTT
1 ATAAAAA-AATATAAATTTTATAATA-ATAAACTTA
* *
4085487 ATAAAAAATTATAAATTGTATAATAA
1 ATAAAAAAATATAAATTTTATAATAA
4085513 CTTTCATAAC
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
34 1 0.02
35 22 0.42
36 27 0.51
37 3 0.06
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (34 bp):
ATAAAAAAATATAAATTTTATAATAATAAACTTA
Found at i:4085481 original size:16 final size:16
Alignment explanation
Indices: 4085460--4085490 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4085450 AATAAAAATA
*
4085460 ATATAAATTTTATAAT
1 ATATAAACTTTATAAT
4085476 ATATAAACTTTATAA
1 ATATAAACTTTATAA
4085491 AAAATTATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
ATATAAACTTTATAAT
Found at i:4085572 original size:20 final size:21
Alignment explanation
Indices: 4085549--4085591 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
4085539 TTATGATAAA
* *
4085549 AAATCATAAT-TTTTTTTTAT
1 AAATAATAATATTATTTTTAT
*
4085569 AAATAATTATATTATTTTTAT
1 AAATAATAATATTATTTTTAT
4085590 AA
1 AA
4085592 TGTATAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
AAATAATAATATTATTTTTAT
Found at i:4085680 original size:25 final size:25
Alignment explanation
Indices: 4085639--4085690 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
4085629 TCCTTAACCC
*
4085639 ATAAATTTTTATAAATAAATATATT
1 ATAAATTTTTATAAATAAATAAATT
*
4085664 ATAATATTTTTAT-AATATATAAATT
1 ATAA-ATTTTTATAAATAAATAAATT
4085689 AT
1 AT
4085691 TTTTTATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
ATAAATTTTTATAAATAAATAAATT
Found at i:4086620 original size:6 final size:6
Alignment explanation
Indices: 4086609--4086639 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
4086599 CTCCCTTCCT
4086609 CCGCCA CCGCCA CCGCCA CCGCCA CCGCCA C
1 CCGCCA CCGCCA CCGCCA CCGCCA CCGCCA C
4086640 GGGCACCAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.68, G:0.16, T:0.00
Consensus pattern (6 bp):
CCGCCA
Found at i:4090528 original size:14 final size:15
Alignment explanation
Indices: 4090509--4090537 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4090499 AAAATAAATA
4090509 TTAA-TTTTACTTTT
1 TTAATTTTTACTTTT
4090523 TTAATTTTTACTTTT
1 TTAATTTTTACTTTT
4090538 AAAAATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (15 bp):
TTAATTTTTACTTTT
Found at i:4092631 original size:3 final size:3
Alignment explanation
Indices: 4092623--4092760 Score: 139
Period size: 3 Copynumber: 48.0 Consensus size: 3
4092613 TTCCATTTTC
* *
4092623 TCT TCT TCT TCT TC- TCAT TC- TCC TCC TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TC-T TCT TCT TCT TCT TCT TCT TCT TCT TCT
* *
4092667 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC- TCC TGT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * *
4092714 TTT TCT TC- TCT GT-T TCT TC- TCT TGT TCT T-T TTT TC- TCT TCT
1 TCT TCT TCT TCT -TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
4092755 TCT TCT
1 TCT TCT
4092761 ATTGCCTAAG
Statistics
Matches: 116, Mismatches: 9, Indels: 20
0.80 0.06 0.14
Matches are distributed among these distances:
2 15 0.13
3 98 0.84
4 3 0.03
ACGTcount: A:0.01, C:0.33, G:0.02, T:0.64
Consensus pattern (3 bp):
TCT
Found at i:4105219 original size:40 final size:40
Alignment explanation
Indices: 4105164--4105243 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
4105154 ATAAGAATAG
*
4105164 GTTTAGATGGACATTACGTTTACTTACAGTTAGTATAAAA
1 GTTTAGATGGACATTACATTTACTTACAGTTAGTATAAAA
*
4105204 GTTTAGATGGACATTATATTTACTTACAGTTAGTATAAAA
1 GTTTAGATGGACATTACATTTACTTACAGTTAGTATAAAA
4105244 ATAGTAGCCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (40 bp):
GTTTAGATGGACATTACATTTACTTACAGTTAGTATAAAA
Found at i:4109043 original size:30 final size:30
Alignment explanation
Indices: 4109004--4109073 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
4108994 TTAAATTAGT
*
4109004 AATAGTAAAATTGTAATTTAACTCCCTAAA
1 AATAATAAAATTGTAATTTAACTCCCTAAA
* * * **
4109034 AATAATAAAATTTTGATTTAATTCTTTAAA
1 AATAATAAAATTGTAATTTAACTCCCTAAA
*
4109064 AATTATAAAA
1 AATAATAAAA
4109074 ATATAGACTA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (30 bp):
AATAATAAAATTGTAATTTAACTCCCTAAA
Found at i:4109321 original size:2 final size:2
Alignment explanation
Indices: 4109316--4109343 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4109306 TGTTTTTTAA
4109316 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4109344 GAATTTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4109611 original size:2 final size:2
Alignment explanation
Indices: 4109604--4109636 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4109594 CTAAGCCATT
4109604 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
4109637 AAGGTTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4111072 original size:38 final size:40
Alignment explanation
Indices: 4111002--4111089 Score: 144
Period size: 38 Copynumber: 2.2 Consensus size: 40
4110992 TAAAAAATAT
*
4111002 TTATATTAAAAACACTACCATAAATATAATAAATATTTTA
1 TTATATTAAAAACACTACAATAAATATAATAAATATTTTA
4111042 TTATATTAAAAACAC-A-AATAAATATAATAAATATTTTA
1 TTATATTAAAAACACTACAATAAATATAATAAATATTTTA
*
4111080 TTGTATTAAA
1 TTATATTAAA
4111090 TATATTTGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
38 30 0.65
39 1 0.02
40 15 0.33
ACGTcount: A:0.53, C:0.07, G:0.01, T:0.39
Consensus pattern (40 bp):
TTATATTAAAAACACTACAATAAATATAATAAATATTTTA
Found at i:4112594 original size:29 final size:29
Alignment explanation
Indices: 4112558--4112616 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
4112548 TGTACTTATT
* *
4112558 AATAAATTTAATGTTTTTTAATTTATAAA
1 AATAAATTTAATATTTTTGAATTTATAAA
* *
4112587 AATAAATTTTATATTTTTGAATTTTTAAA
1 AATAAATTTAATATTTTTGAATTTATAAA
4112616 A
1 A
4112617 TTTTAAAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (29 bp):
AATAAATTTAATATTTTTGAATTTATAAA
Found at i:4112984 original size:8 final size:8
Alignment explanation
Indices: 4112971--4113007 Score: 74
Period size: 8 Copynumber: 4.6 Consensus size: 8
4112961 TTATGTTTAG
4112971 TATATTAT
1 TATATTAT
4112979 TATATTAT
1 TATATTAT
4112987 TATATTAT
1 TATATTAT
4112995 TATATTAT
1 TATATTAT
4113003 TATAT
1 TATAT
4113008 AATAAAGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATATTAT
Found at i:4113040 original size:5 final size:5
Alignment explanation
Indices: 4113030--4113071 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
4113020 TAATGTTTTA
4113030 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
4113072 ATAAACTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:4114360 original size:15 final size:15
Alignment explanation
Indices: 4114340--4114396 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
4114330 GCATGAATTT
4114340 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
4114355 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
4114370 ATTGAATTTATATTG
1 ATTGAATTTATATTG
4114385 ATTGAA-TTATAT
1 ATTGAATTTATAT
4114397 AATATACATG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:4114801 original size:23 final size:22
Alignment explanation
Indices: 4114765--4114828 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 22
4114755 ATTTATCGAC
* *
4114765 AGGCACTTTATGTGTCGTATTT
1 AGGCACCTCATGTGTCGTATTT
*
4114787 CAGGCACCTCGTGTGTCGT-TTT
1 -AGGCACCTCATGTGTCGTATTT
* *
4114809 AGGCACTTTATGTGTCGTAT
1 AGGCACCTCATGTGTCGTAT
4114829 ACTGATCAGG
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 15 0.44
22 4 0.12
23 15 0.44
ACGTcount: A:0.16, C:0.19, G:0.25, T:0.41
Consensus pattern (22 bp):
AGGCACCTCATGTGTCGTATTT
Found at i:4114822 original size:21 final size:23
Alignment explanation
Indices: 4114764--4114828 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
4114754 GATTTATCGA
4114764 CAGGCACTTTATGTGTCGTATTT
1 CAGGCACTTTATGTGTCGTATTT
* **
4114787 CAGGCACCTCGTGTGTCGT-TTT
1 CAGGCACTTTATGTGTCGTATTT
4114809 -AGGCACTTTATGTGTCGTAT
1 CAGGCACTTTATGTGTCGTAT
4114829 ACTGATCAGG
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
21 15 0.43
22 4 0.11
23 16 0.46
ACGTcount: A:0.15, C:0.20, G:0.25, T:0.40
Consensus pattern (23 bp):
CAGGCACTTTATGTGTCGTATTT
Found at i:4117478 original size:38 final size:39
Alignment explanation
Indices: 4117427--4117514 Score: 124
Period size: 38 Copynumber: 2.3 Consensus size: 39
4117417 AAAAATTATA
* * *
4117427 TTTAATACAATAAAACATTTATTATATTTAT-TTGTGTT
1 TTTAATATAATAAAACATTCATTATATTTATATAGTGTT
*
4117465 TTTAATATAATAAAACATTCGTTATATTTATAATAGTGTT
1 TTTAATATAATAAAACATTCATTATATTTAT-ATAGTGTT
4117505 TTTAATATAA
1 TTTAATATAA
4117515 ATATTTTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
38 28 0.64
40 16 0.36
ACGTcount: A:0.40, C:0.05, G:0.06, T:0.50
Consensus pattern (39 bp):
TTTAATATAATAAAACATTCATTATATTTATATAGTGTT
Found at i:4121528 original size:17 final size:17
Alignment explanation
Indices: 4121503--4121538 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
4121493 AAGTTGACTT
* *
4121503 GAACTTAAAACCAATTC
1 GAACCTAAAAACAATTC
4121520 GAACCTAAAAACAATTC
1 GAACCTAAAAACAATTC
4121537 GA
1 GA
4121539 CCAAGTTAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.50, C:0.22, G:0.08, T:0.19
Consensus pattern (17 bp):
GAACCTAAAAACAATTC
Found at i:4121562 original size:48 final size:48
Alignment explanation
Indices: 4121491--4121586 Score: 156
Period size: 48 Copynumber: 2.0 Consensus size: 48
4121481 CAACCCATAC
* * * *
4121491 CCAAGTTGACTTGAACTTAAAACCAATTCGAACCTAAAAACAATTCGA
1 CCAAGTTAACTTGAACTTAAAACCAATCCAAACCCAAAAACAATTCGA
4121539 CCAAGTTAACTTGAACTTAAAACCAATCCAAACCCAAAAACAATTCGA
1 CCAAGTTAACTTGAACTTAAAACCAATCCAAACCCAAAAACAATTCGA
4121587 AAGTAATTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.46, C:0.25, G:0.08, T:0.21
Consensus pattern (48 bp):
CCAAGTTAACTTGAACTTAAAACCAATCCAAACCCAAAAACAATTCGA
Found at i:4122654 original size:16 final size:16
Alignment explanation
Indices: 4122633--4122665 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
4122623 CTTATGCCTT
4122633 CAATGAACCCATTCAA
1 CAATGAACCCATTCAA
*
4122649 CAATGACCCCATTCAA
1 CAATGAACCCATTCAA
4122665 C
1 C
4122666 TCAATACAAC
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:0.39, C:0.36, G:0.06, T:0.18
Consensus pattern (16 bp):
CAATGAACCCATTCAA
Found at i:4124942 original size:14 final size:14
Alignment explanation
Indices: 4124923--4124953 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
4124913 AAAAATTCAT
*
4124923 ATAAATTTGTAATA
1 ATAAATTTATAATA
4124937 ATAAATTTATAATA
1 ATAAATTTATAATA
4124951 ATA
1 ATA
4124954 CTTTAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (14 bp):
ATAAATTTATAATA
Found at i:4138483 original size:4 final size:4
Alignment explanation
Indices: 4138474--4138505 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
4138464 GTTTTTACAG
4138474 CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA
4138506 TGTTCATACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:4145201 original size:22 final size:22
Alignment explanation
Indices: 4145173--4145217 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
4145163 TCTTGATATT
4145173 ATATATCACAAAATGTAAAGAA
1 ATATATCACAAAATGTAAAGAA
4145195 ATATATCACAAAATGTAAAGAA
1 ATATATCACAAAATGTAAAGAA
4145217 A
1 A
4145218 ATAATTGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.60, C:0.09, G:0.09, T:0.22
Consensus pattern (22 bp):
ATATATCACAAAATGTAAAGAA
Found at i:4145407 original size:17 final size:18
Alignment explanation
Indices: 4145375--4145408 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4145365 TATCAATGTC
*
4145375 TTCAAAAAATACTTTTCA
1 TTCAAAAAATAATTTTCA
4145393 TTCAAAAAA-AATTTTC
1 TTCAAAAAATAATTTTC
4145409 TTTTAAATTA
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:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (18 bp):
TTCAAAAAATAATTTTCA
Found at i:4145587 original size:11 final size:11
Alignment explanation
Indices: 4145571--4145601 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
4145561 CACGGTAACA
4145571 ATTTCTTCTTC
1 ATTTCTTCTTC
4145582 ATTTCTTCTTC
1 ATTTCTTCTTC
*
4145593 AGTTCTTCT
1 ATTTCTTCT
4145602 CTCTGGTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.10, C:0.26, G:0.03, T:0.61
Consensus pattern (11 bp):
ATTTCTTCTTC
Found at i:4145961 original size:13 final size:13
Alignment explanation
Indices: 4145944--4146005 Score: 79
Period size: 13 Copynumber: 4.7 Consensus size: 13
4145934 TTAAACAAAA
4145944 TTTTTCAAAAGTAC
1 TTTTT-AAAAGTAC
*
4145958 TTTTTAAAAGTAT
1 TTTTTAAAAGTAC
* **
4145971 TTTTTCACTGTAC
1 TTTTTAAAAGTAC
4145984 TTTTTAAAAGTAC
1 TTTTTAAAAGTAC
4145997 TTTTTAAAA
1 TTTTTAAAA
4146006 ACAACGCTAA
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
13 35 0.88
14 5 0.12
ACGTcount: A:0.34, C:0.10, G:0.06, T:0.50
Consensus pattern (13 bp):
TTTTTAAAAGTAC
Found at i:4146192 original size:14 final size:15
Alignment explanation
Indices: 4146156--4146194 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
4146146 TTACACTCTT
4146156 TTTTGTTTTTAAAAG
1 TTTTGTTTTTAAAAG
*
4146171 TTTT-TTTTTTAAA-
1 TTTTGTTTTTAAAAG
4146184 TTTTGTTTTTA
1 TTTTGTTTTTA
4146195 CTACCATCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 4 0.19
14 13 0.62
15 4 0.19
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.72
Consensus pattern (15 bp):
TTTTGTTTTTAAAAG
Found at i:4150984 original size:21 final size:21
Alignment explanation
Indices: 4150954--4150994 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4150944 AAGTAAGAGC
* *
4150954 AAATTTTTTTATTTTTAAATA
1 AAATTATTTTAATTTTAAATA
4150975 AAATTATTTTAATTTTAAAT
1 AAATTATTTTAATTTTAAAT
4150995 CTATTGATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
AAATTATTTTAATTTTAAATA
Found at i:4162489 original size:485 final size:485
Alignment explanation
Indices: 4161580--4162554 Score: 1878
Period size: 485 Copynumber: 2.0 Consensus size: 485
4161570 ATTTATATTT
4161580 AAATTCGGGTTCGGCTTAAGGTGTATTCCAGTTCAAGTTTAAGCTAGGTTCGATAATTAAATTTG
1 AAATTCGGGTTCGGCTTAAGGTGTATTCCAGTTCAAGTTTAAGCTAGGTTCGATAATTAAATTTG
4161645 AAAAATTTAGTAAGGCTTGCAAATCGTTCAAGTTGAGCATTATTAAGCTTGAACTAGTTCGAACT
66 AAAAATTTAGTAAGGCTTGCAAATCGTTCAAGTTGAGCATTATTAAGCTTGAACTAGTTCGAACT
* *
4161710 ATAGGTCAAGCTATTTGGGCTTGATTTCGTATTTATTGAATTAATTTTTTTAAATCAAACTCAAA
131 ATAAGTCAAGCTATTTGGGCTTGATTCCGTATTTATTGAATTAATTTTTTTAAATCAAACTCAAA
*
4161775 ATTTACGATTTTCACTTAAATTTTAGGTTCCAACTGATTCACGGCAGTCAAGATTGCAAATTTGA
196 ATTTACGATTTTCACTTAAATTTTAGGGTCCAACTGATTCACGGCAGTCAAGATTGCAAATTTGA
4161840 ATATACGTAGGTATTCAATCTATTTTCTGCGGGGTGCAAATATTTAGAATTATATTTTAAGATTA
261 ATATACGTAGGTATTCAATCTATTTTCTGCGGGGTGCAAATATTTAGAATTATATTTTAAGATTA
4161905 TTTTTCATTTCGAATTCAGATATCAAATCCATCTTATAATTTTAATTTTTTATTTTGATATTCGA
326 TTTTTCATTTCGAATTCAGATATCAAATCCATCTTATAATTTTAATTTTTTATTTTGATATTCGA
* *
4161970 AAAATGATTAGAAATTTTAAATATTCAACTGATAATAATAAATAATTCAGTCTTGATTAAACATA
391 AAAATGATTAGAAATTTTAAATATCCAACTGATAATAATAAATAATTCAATCTTGATTAAACATA
4162035 TTCAAACTTATAGATAAGTATAGGAATCCA
456 TTCAAACTTATAGATAAGTATAGGAATCCA
*
4162065 AAATTCGGGTTCGGCTTAAGGTGTATTCCAGTTCAAGTTTAAGCTAGGTTCGATAATTAAGTTTG
1 AAATTCGGGTTCGGCTTAAGGTGTATTCCAGTTCAAGTTTAAGCTAGGTTCGATAATTAAATTTG
4162130 AAAAATTTAGTAAGGCTTGCAAATCGTTCAAGTTGAGCATTATTAAGCTTGAACTAGTTCGAACT
66 AAAAATTTAGTAAGGCTTGCAAATCGTTCAAGTTGAGCATTATTAAGCTTGAACTAGTTCGAACT
4162195 ATAAGTCAAGCTATTTGGGCTTGATTCCGTATTTATTGAATTAATTTTTTTAAATCAAACTCAAA
131 ATAAGTCAAGCTATTTGGGCTTGATTCCGTATTTATTGAATTAATTTTTTTAAATCAAACTCAAA
*
4162260 ATTTACGATTTTCACTTAAATTTTAGGGTCCAACTGATTCACTGCAGTCAAGATTGCAAATTTGA
196 ATTTACGATTTTCACTTAAATTTTAGGGTCCAACTGATTCACGGCAGTCAAGATTGCAAATTTGA
4162325 ATATACGTAGGTATTCAATCTATTTTCTGCGGGGTGCAAATATTTAGAATTATATTTTAAGATTA
261 ATATACGTAGGTATTCAATCTATTTTCTGCGGGGTGCAAATATTTAGAATTATATTTTAAGATTA
4162390 TTTTTCATTTCGAATTCAGATATCAAATCCATCTTATAATTTTAATTTTTTATTTTGATATTCGA
326 TTTTTCATTTCGAATTCAGATATCAAATCCATCTTATAATTTTAATTTTTTATTTTGATATTCGA
4162455 AAAATGATTAGAAATTTTAAATATCCAACTGATAATAATAAATAATTCAATCTTGATTAAACATA
391 AAAATGATTAGAAATTTTAAATATCCAACTGATAATAATAAATAATTCAATCTTGATTAAACATA
*
4162520 TTTAAACTTATAGATAAGTATAGGAATCCA
456 TTCAAACTTATAGATAAGTATAGGAATCCA
4162550 AAATT
1 AAATT
4162555 AGATAAATCA
Statistics
Matches: 482, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
485 482 1.00
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (485 bp):
AAATTCGGGTTCGGCTTAAGGTGTATTCCAGTTCAAGTTTAAGCTAGGTTCGATAATTAAATTTG
AAAAATTTAGTAAGGCTTGCAAATCGTTCAAGTTGAGCATTATTAAGCTTGAACTAGTTCGAACT
ATAAGTCAAGCTATTTGGGCTTGATTCCGTATTTATTGAATTAATTTTTTTAAATCAAACTCAAA
ATTTACGATTTTCACTTAAATTTTAGGGTCCAACTGATTCACGGCAGTCAAGATTGCAAATTTGA
ATATACGTAGGTATTCAATCTATTTTCTGCGGGGTGCAAATATTTAGAATTATATTTTAAGATTA
TTTTTCATTTCGAATTCAGATATCAAATCCATCTTATAATTTTAATTTTTTATTTTGATATTCGA
AAAATGATTAGAAATTTTAAATATCCAACTGATAATAATAAATAATTCAATCTTGATTAAACATA
TTCAAACTTATAGATAAGTATAGGAATCCA
Found at i:4166090 original size:2 final size:2
Alignment explanation
Indices: 4166083--4166117 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4166073 AGTAAGCTAT
4166083 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
4166118 TATATATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:4172041 original size:31 final size:31
Alignment explanation
Indices: 4171945--4172041 Score: 88
Period size: 31 Copynumber: 3.1 Consensus size: 31
4171935 AACAACAGAG
** *
4171945 TGACTTAAATAAAAAACTTTCGAAT-AGTCCAA
1 TGACTTAAATAAAAAA-TTTTAAATAAAT-CAA
* ** * * *
4171977 TGACTCAAGCAAAAATTTTTAAATAATTTAA
1 TGACTTAAATAAAAAATTTTAAATAAATCAA
4172008 TGACTTAAATAAAAAATTTTAAATAAATCAA
1 TGACTTAAATAAAAAATTTTAAATAAATCAA
4172039 TGA
1 TGA
4172042 TATTTTTTAA
Statistics
Matches: 50, Mismatches: 14, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
31 36 0.72
32 14 0.28
ACGTcount: A:0.51, C:0.10, G:0.07, T:0.32
Consensus pattern (31 bp):
TGACTTAAATAAAAAATTTTAAATAAATCAA
Found at i:4172997 original size:1 final size:1
Alignment explanation
Indices: 4172950--4172978 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
4172940 CATTTCCCTT
4172950 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4172979 GGTAGATGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4178228 original size:14 final size:15
Alignment explanation
Indices: 4178209--4178237 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
4178199 CAAATAGAAT
4178209 TATAATTTT-TTAAA
1 TATAATTTTGTTAAA
4178223 TATAATTTTGTTAAA
1 TATAATTTTGTTAAA
4178238 CAATAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TATAATTTTGTTAAA
Found at i:4180878 original size:6 final size:6
Alignment explanation
Indices: 4180867--4180892 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
4180857 GATGAGTCAT
4180867 TGGCAA TGGCAA TGGCAA TGGCAA TG
1 TGGCAA TGGCAA TGGCAA TGGCAA TG
4180893 CCACCGCCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.15, G:0.35, T:0.19
Consensus pattern (6 bp):
TGGCAA
Done.