Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 5 of 226
Found at i:1726517 original size:20 final size:19
Alignment explanation
Indices: 1726494--1726541 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 19
1726484 ATAATAAATT
1726494 ACATAATACTTTATATAATA
1 ACATAATAC-TTATATAATA
1726514 ACATAATAACTTATATAATA
1 ACATAAT-ACTTATATAATA
1726534 ACATAATA
1 ACATAATA
1726542 ACTAACATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.04
20 24 0.89
21 2 0.07
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.35
Consensus pattern (19 bp):
ACATAATACTTATATAATA
Found at i:1726636 original size:9 final size:9
Alignment explanation
Indices: 1726599--1727180 Score: 592
Period size: 9 Copynumber: 66.4 Consensus size: 9
1726589 TAATAACATA
*
1726599 ATAACTAAC
1 ATAACTTAC
1726608 ATAA--TAC
1 ATAACTTAC
* *
1726615 ATAACCTAA
1 ATAACTTAC
1726624 ATAACTTAC
1 ATAACTTAC
1726633 ATAACTTAC
1 ATAACTTAC
1726642 ATAACTTAC
1 ATAACTTAC
*
1726651 ATTA--TAC
1 ATAACTTAC
*
1726658 ACAACTTAC
1 ATAACTTAC
* *
1726667 ATAAATTAA
1 ATAACTTAC
1726676 ATAACTTAC
1 ATAACTTAC
1726685 ATAACTTAC
1 ATAACTTAC
*
1726694 AT-ACATTAA
1 ATAAC-TTAC
1726703 ATAACTTAC
1 ATAACTTAC
1726712 ATAACTTAC
1 ATAACTTAC
1726721 ATAACTTAC
1 ATAACTTAC
*
1726730 ATTA--TAC
1 ATAACTTAC
*
1726737 ACAACTTAC
1 ATAACTTAC
* *
1726746 ATAAATTAA
1 ATAACTTAC
1726755 ATAACTTAC
1 ATAACTTAC
1726764 ATAACTTAC
1 ATAACTTAC
*
1726773 ATAAGTTAC
1 ATAACTTAC
* *
1726782 ATAAATTAA
1 ATAACTTAC
1726791 ATAACTTAC
1 ATAACTTAC
1726800 ATAACTTAC
1 ATAACTTAC
* *
1726809 ATAAATTAA
1 ATAACTTAC
1726818 ATAACTTAC
1 ATAACTTAC
1726827 ATAACTTAC
1 ATAACTTAC
* *
1726836 ATAAATTAA
1 ATAACTTAC
1726845 ATAACTTAC
1 ATAACTTAC
1726854 ATAACTTAC
1 ATAACTTAC
1726863 ATAACTTAC
1 ATAACTTAC
* *
1726872 ATAAATTAA
1 ATAACTTAC
1726881 ATAACTTAC
1 ATAACTTAC
1726890 ATAACTTAC
1 ATAACTTAC
1726899 ATAACTTAC
1 ATAACTTAC
* *
1726908 ATAAATTAA
1 ATAACTTAC
1726917 ATAACTTAC
1 ATAACTTAC
*
1726926 ATAAGTTAC
1 ATAACTTAC
* *
1726935 ATAAATTAA
1 ATAACTTAC
*
1726944 ATAACTTTC
1 ATAACTTAC
1726953 ATAACTTAC
1 ATAACTTAC
*
1726962 ATAAGTTAC
1 ATAACTTAC
* *
1726971 ATAAATTAA
1 ATAACTTAC
*
1726980 ATAACTTTC
1 ATAACTTAC
1726989 ATAACTTAC
1 ATAACTTAC
1726998 ATAACTTAC
1 ATAACTTAC
* *
1727007 ATAAATTAA
1 ATAACTTAC
1727016 ATAACTTAC
1 ATAACTTAC
1727025 ATAACTTAC
1 ATAACTTAC
* *
1727034 ATAAATTAA
1 ATAACTTAC
1727043 ATAACTTAC
1 ATAACTTAC
1727052 ATAACTTAC
1 ATAACTTAC
*
1727061 ATTA--TAC
1 ATAACTTAC
1727068 ATAACCTT-C
1 ATAA-CTTAC
*
1727077 TTAACTTAC
1 ATAACTTAC
*
1727086 ATTA--TAC
1 ATAACTTAC
* *
1727093 ACAACTCAC
1 ATAACTTAC
1727102 ATAA-TTA-
1 ATAACTTAC
*
1727109 AT-ATTATAC
1 ATAACT-TAC
*
1727118 ACAACTTAC
1 ATAACTTAC
*
1727127 ATAACTTTC
1 ATAACTTAC
*
1727136 ATTACTTAC
1 ATAACTTAC
1727145 AGT-ACTTAC
1 A-TAACTTAC
1727154 ATAA--TAC
1 ATAACTTAC
1727161 ATAA--TAC
1 ATAACTTAC
1727168 ATAACTTAC
1 ATAACTTAC
1727177 ATAA
1 ATAA
1727181 TACATAAAAA
Statistics
Matches: 470, Mismatches: 81, Indels: 44
0.79 0.14 0.07
Matches are distributed among these distances:
6 1 0.00
7 44 0.09
8 10 0.02
9 409 0.87
10 6 0.01
ACGTcount: A:0.48, C:0.18, G:0.01, T:0.34
Consensus pattern (9 bp):
ATAACTTAC
Found at i:1727163 original size:7 final size:7
Alignment explanation
Indices: 1727151--1727187 Score: 56
Period size: 7 Copynumber: 5.0 Consensus size: 7
1727141 TTACAGTACT
1727151 TACATAA
1 TACATAA
1727158 TACATAA
1 TACATAA
1727165 TACATAA
1 TACATAA
1727172 CTTACATAA
1 --TACATAA
1727181 TACATAA
1 TACATAA
1727188 AAATATATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 21 0.75
9 7 0.25
ACGTcount: A:0.54, C:0.16, G:0.00, T:0.30
Consensus pattern (7 bp):
TACATAA
Found at i:1729441 original size:20 final size:19
Alignment explanation
Indices: 1729405--1729460 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
1729395 ATTTTGAATT
*
1729405 TTTTTATATATTCTTTAGAA
1 TTTTTATAT-TTTTTTAGAA
*
1729425 TTTTTAATATTTTTTTAAAA
1 TTTTT-ATATTTTTTTAGAA
* *
1729445 TTATTATAATTTTTTA
1 TTTTTATATTTTTTTA
1729461 AAAAATATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 10 0.32
20 17 0.55
21 4 0.13
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTTTATATTTTTTTAGAA
Found at i:1738417 original size:24 final size:24
Alignment explanation
Indices: 1738390--1738436 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1738380 ATTACACCTT
*
1738390 ATATTACAGGATGATCGTAATGTG
1 ATATTACAGGATGATCGGAATGTG
*
1738414 ATATTACAGGATGGTCGGAATGT
1 ATATTACAGGATGATCGGAATGT
1738437 TGAAATCCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.32, C:0.09, G:0.28, T:0.32
Consensus pattern (24 bp):
ATATTACAGGATGATCGGAATGTG
Found at i:1759013 original size:22 final size:22
Alignment explanation
Indices: 1758971--1759014 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1758961 CCTAACGTAT
* *
1758971 AAAAATTAATTTATCTATTTAA
1 AAAAATTAATCTAACTATTTAA
1758993 AAAAATTCAATCTAACT-TTTAA
1 AAAAATT-AATCTAACTATTTAA
1759015 TTTAATAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAAATTAATCTAACTATTTAA
Found at i:1792282 original size:22 final size:22
Alignment explanation
Indices: 1792257--1792328 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
1792247 TGCCTAAACC
1792257 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
1792279 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
** *
1792301 CTCATGTTTCACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
1792323 CTCATG
1 CTCATG
1792329 TTTGAACAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.31
Consensus pattern (22 bp):
CTCATGGCTAACGTACTAAGCT
Found at i:1805534 original size:13 final size:13
Alignment explanation
Indices: 1805516--1805540 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1805506 TTTTGCTTCC
1805516 TTTTTCCTTTTTA
1 TTTTTCCTTTTTA
1805529 TTTTTCCTTTTT
1 TTTTTCCTTTTT
1805541 CCCGCCGTAA
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:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTCCTTTTTA
Found at i:1812365 original size:28 final size:28
Alignment explanation
Indices: 1812332--1812392 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
1812322 ATTAAAGGGA
*
1812332 TTAAATTAGAATTTTAGTAT-TTTTAAGT
1 TTAAATTAGAATTTTAGTATATATTAA-T
* *
1812360 TTAAATTATAATTTTATTATATATTAAT
1 TTAAATTAGAATTTTAGTATATATTAAT
1812388 TTAAA
1 TTAAA
1812393 ATTTTATGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 24 0.83
29 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (28 bp):
TTAAATTAGAATTTTAGTATATATTAAT
Found at i:1815095 original size:21 final size:21
Alignment explanation
Indices: 1815062--1815105 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1815052 AGGAGGGGAG
*
1815062 TGTGGAGGCGGTGGTGGAGAA
1 TGTGGAGGCGGTGGGGGAGAA
* * *
1815083 TGTGGTGGGGGTGGGGGTGAA
1 TGTGGAGGCGGTGGGGGAGAA
1815104 TG
1 TG
1815106 ATGTGGCGGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.02, G:0.61, T:0.23
Consensus pattern (21 bp):
TGTGGAGGCGGTGGGGGAGAA
Found at i:1815111 original size:21 final size:21
Alignment explanation
Indices: 1815068--1815141 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
1815058 GGAGTGTGGA
* *
1815068 GGCGGTGGTGGAGAATG-TGGT
1 GGCGGTGGAGGTGAATGAT-GT
* *
1815089 GGGGGTGGGGGTGAATGATGT
1 GGCGGTGGAGGTGAATGATGT
*
1815110 GGCGGTGGAGGTGACTGATGT
1 GGCGGTGGAGGTGAATGATGT
*
1815131 GGTGGTGGAGG
1 GGCGGTGGAGG
1815142 GGAGTTATAG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 44 0.98
22 1 0.02
ACGTcount: A:0.14, C:0.04, G:0.59, T:0.23
Consensus pattern (21 bp):
GGCGGTGGAGGTGAATGATGT
Found at i:1815290 original size:39 final size:39
Alignment explanation
Indices: 1815247--1815354 Score: 144
Period size: 39 Copynumber: 2.8 Consensus size: 39
1815237 ATATTGGCGC
* *
1815247 AGGTGGTGGGGGTGAAGGGGGCGGTGGTGACGGATAAGT
1 AGGTGGTGGGGGTGAAGGAGGTGGTGGTGACGGATAAGT
* * * * *
1815286 AGGTGGCGGGGGTGAAGGTGGTGGAGGTGATGGATATGT
1 AGGTGGTGGGGGTGAAGGAGGTGGTGGTGACGGATAAGT
*
1815325 AGGGGGTGGGGGTGAAGGAGGTGGTGGTGA
1 AGGTGGTGGGGGTGAAGGAGGTGGTGGTGA
1815355 GGGCGGTGGA
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 59 1.00
ACGTcount: A:0.18, C:0.03, G:0.60, T:0.19
Consensus pattern (39 bp):
AGGTGGTGGGGGTGAAGGAGGTGGTGGTGACGGATAAGT
Found at i:1815353 original size:15 final size:15
Alignment explanation
Indices: 1815329--1815395 Score: 53
Period size: 15 Copynumber: 4.5 Consensus size: 15
1815319 ATATGTAGGG
*
1815329 GGTGGGGGTGAAGGA
1 GGTGGAGGTGAAGGA
* * *
1815344 GGTGGTGGTGAGGGC
1 GGTGGAGGTGAAGGA
* *
1815359 GGTGGAGGTGATGGT
1 GGTGGAGGTGAAGGA
* **
1815374 GGTGGAGGAGGTGGA
1 GGTGGAGGTGAAGGA
1815389 GGTGGAG
1 GGTGGAG
1815396 AGTAAACAGG
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 43 1.00
ACGTcount: A:0.15, C:0.01, G:0.66, T:0.18
Consensus pattern (15 bp):
GGTGGAGGTGAAGGA
Found at i:1815386 original size:24 final size:24
Alignment explanation
Indices: 1815346--1815392 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1815336 GTGAAGGAGG
*
1815346 TGGTGGTGAGGGCGGTGGAGGTGA
1 TGGTGGTGAGGGAGGTGGAGGTGA
1815370 TGGTGGTG-GAGGAGGTGGAGGTG
1 TGGTGGTGAG-GGAGGTGGAGGTG
1815393 GAGAGTAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.13, C:0.02, G:0.64, T:0.21
Consensus pattern (24 bp):
TGGTGGTGAGGGAGGTGGAGGTGA
Found at i:1815504 original size:30 final size:27
Alignment explanation
Indices: 1815452--1815510 Score: 73
Period size: 30 Copynumber: 2.1 Consensus size: 27
1815442 GGGCGGTGGT
*
1815452 GGGGGAGGTGAAAAAACTGGTGGGGGA
1 GGGGGAGGTGAAAAAACGGGTGGGGGA
*
1815479 GGGGGAGGTGGAGAGAAAACGGGTGGTGGA
1 GGGGGAGGT-GA-A-AAAACGGGTGGGGGA
1815509 GG
1 GG
1815511 TGAAGGAGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 9 0.33
28 2 0.07
29 1 0.04
30 15 0.56
ACGTcount: A:0.27, C:0.03, G:0.59, T:0.10
Consensus pattern (27 bp):
GGGGGAGGTGAAAAAACGGGTGGGGGA
Found at i:1817417 original size:5 final size:5
Alignment explanation
Indices: 1817404--1817435 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
1817394 CAGAGAGACA
*
1817404 TGGGG TGGGT TGGGT TGGGT TGGGT TGGGT TG
1 TGGGT TGGGT TGGGT TGGGT TGGGT TGGGT TG
1817436 TTGATATCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.62, T:0.38
Consensus pattern (5 bp):
TGGGT
Found at i:1836231 original size:16 final size:17
Alignment explanation
Indices: 1836212--1836244 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1836202 TAATTCTTTG
1836212 TAATTAC-AAGAGAGTA
1 TAATTACTAAGAGAGTA
1836228 TAATTACTAAGAGAGTA
1 TAATTACTAAGAGAGTA
1836245 ATTGCACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.27
Consensus pattern (17 bp):
TAATTACTAAGAGAGTA
Found at i:1836486 original size:2 final size:2
Alignment explanation
Indices: 1836479--1836511 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1836469 NNNNNNNNNN
1836479 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1836512 AAATTGATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1841185 original size:24 final size:24
Alignment explanation
Indices: 1841158--1841204 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1841148 CGGTGCTTCC
1841158 CGTTAATTGCTCTTCGGAGCTACT
1 CGTTAATTGCTCTTCGGAGCTACT
*
1841182 CGTTAATTGCTCTTTGGAGCTAC
1 CGTTAATTGCTCTTCGGAGCTAC
1841205 CCATTATAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.38
Consensus pattern (24 bp):
CGTTAATTGCTCTTCGGAGCTACT
Found at i:1847264 original size:28 final size:29
Alignment explanation
Indices: 1847228--1847292 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 29
1847218 GACCAAAAAA
* * *
1847228 GCCTTTTTTTTTA-AATTTATCGAAATGG
1 GCCTATTTTTTGATAATTTACCGAAATGG
* *
1847256 GCCTATTTTTTGATTATTTACCGGAATGG
1 GCCTATTTTTTGATAATTTACCGAAATGG
1847285 GCC-ATTTT
1 GCCTATTTT
1847293 CCGCGAAATC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 16 0.52
29 15 0.48
ACGTcount: A:0.22, C:0.14, G:0.17, T:0.48
Consensus pattern (29 bp):
GCCTATTTTTTGATAATTTACCGAAATGG
Found at i:1861968 original size:80 final size:80
Alignment explanation
Indices: 1861835--1861994 Score: 320
Period size: 80 Copynumber: 2.0 Consensus size: 80
1861825 TTGTAAACTG
1861835 CAGTTGCTTCTTCCGAATACCAAACTTCAGGACACTGTCCTCCCATAGCAAATGGATGAAATATA
1 CAGTTGCTTCTTCCGAATACCAAACTTCAGGACACTGTCCTCCCATAGCAAATGGATGAAATATA
1861900 CAGATTTTTCAACCA
66 CAGATTTTTCAACCA
1861915 CAGTTGCTTCTTCCGAATACCAAACTTCAGGACACTGTCCTCCCATAGCAAATGGATGAAATATA
1 CAGTTGCTTCTTCCGAATACCAAACTTCAGGACACTGTCCTCCCATAGCAAATGGATGAAATATA
1861980 CAGATTTTTCAACCA
66 CAGATTTTTCAACCA
1861995 TTTATCCTGA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.28
Consensus pattern (80 bp):
CAGTTGCTTCTTCCGAATACCAAACTTCAGGACACTGTCCTCCCATAGCAAATGGATGAAATATA
CAGATTTTTCAACCA
Found at i:1863383 original size:56 final size:56
Alignment explanation
Indices: 1863311--1863422 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
1863301 ATTCCAAAAA
1863311 GAAACAGCAATGGTTGGCTTTTCATGACCACCTTACCTACTTATTCCATCTTCATC
1 GAAACAGCAATGGTTGGCTTTTCATGACCACCTTACCTACTTATTCCATCTTCATC
1863367 GAAACAGCAATGGTTGGCTTTTCATGACCACCTTACCTACTTATTCCATCTTCATC
1 GAAACAGCAATGGTTGGCTTTTCATGACCACCTTACCTACTTATTCCATCTTCATC
1863423 TTTTTTTTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.25, C:0.29, G:0.12, T:0.34
Consensus pattern (56 bp):
GAAACAGCAATGGTTGGCTTTTCATGACCACCTTACCTACTTATTCCATCTTCATC
Found at i:1866758 original size:30 final size:30
Alignment explanation
Indices: 1866701--1866758 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
1866691 AAGAACATAC
* *
1866701 AGAAAATAGTTTAAAACTCTACCAATTTAA
1 AGAAAATAGTTAAAAACTCTACAAATTTAA
*
1866731 AGAAAA-AGTTAAAAACTTTAACAAATTT
1 AGAAAATAGTTAAAAACTCT-ACAAATTT
1866759 CAGCATCAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.29
Consensus pattern (30 bp):
AGAAAATAGTTAAAAACTCTACAAATTTAA
Found at i:1871770 original size:3 final size:3
Alignment explanation
Indices: 1871762--1871837 Score: 59
Period size: 3 Copynumber: 25.7 Consensus size: 3
1871752 TTACTTTATT
** **
1871762 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA -AA CCA TAA TAA TGGT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
* *
1871809 TAA TAA TTA TAA TAA TTA T-A TATA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TA
1871838 TTTATGTATA
Statistics
Matches: 58, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
2 6 0.10
3 48 0.83
4 4 0.07
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1872476 original size:28 final size:28
Alignment explanation
Indices: 1872418--1872478 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
1872408 AAACTATTTC
* *
1872418 ATAATTATTAAAAACTCGGAATAACTTA
1 ATAATTATTAAAAACTCAGAATAACTAA
*
1872446 ATAATTATTAAAAATTCAGAATAA-TAAA
1 ATAATTATTAAAAACTCAGAATAACT-AA
1872474 ATAAT
1 ATAAT
1872479 GAGAGTTGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 1 0.03
28 28 0.97
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.33
Consensus pattern (28 bp):
ATAATTATTAAAAACTCAGAATAACTAA
Found at i:1875769 original size:8 final size:8
Alignment explanation
Indices: 1875756--1875784 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1875746 AATTTCTGTC
1875756 ATTATTAT
1 ATTATTAT
1875764 ATTATTAT
1 ATTATTAT
1875772 ATTATTAT
1 ATTATTAT
1875780 -TTATT
1 ATTATT
1875785 TGTTTCTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 5 0.24
8 16 0.76
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
ATTATTAT
Found at i:1885142 original size:21 final size:22
Alignment explanation
Indices: 1885118--1885177 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
1885108 TATAACTCTA
1885118 AAAATAAAAATATATTT-TAAT
1 AAAATAAAAATATATTTATAAT
*
1885139 AAAA-ACAAAATATTTTTATAAT
1 AAAATA-AAAATATATTTATAAT
*
1885161 AAAAT-AAAATCTATTTA
1 AAAATAAAAATATATTTA
1885178 ATCTTTAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.03
21 24 0.73
22 8 0.24
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAATAAAAATATATTTATAAT
Found at i:1889342 original size:29 final size:30
Alignment explanation
Indices: 1889310--1889371 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 30
1889300 AAAGTATTTT
1889310 AAAAATATTTTAAAATT-AAAAAATTAAAA
1 AAAAATATTTTAAAATTAAAAAAATTAAAA
*
1889339 AAAAGTATTTTAAAATTAAAAAAAATTAAAA
1 AAAAATATTTTAAAATT-AAAAAAATTAAAA
1889370 AA
1 AA
1889372 GTATGTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 16 0.53
31 14 0.47
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (30 bp):
AAAAATATTTTAAAATTAAAAAAATTAAAA
Found at i:1889371 original size:40 final size:39
Alignment explanation
Indices: 1889285--1889406 Score: 129
Period size: 40 Copynumber: 3.0 Consensus size: 39
1889275 TTTAAAAATT
* ***
1889285 TTAAAAAATTAAAAAAAAGTATTTTAAAAATATTTTAAAA
1 TTAAAAAATTAAAAAAAAGTATTTTAAAATTA-AAAAAAA
1889325 TTAAAAAATTAAAAAAAAGTATTTTAAAATTAAAAAAAA
1 TTAAAAAATTAAAAAAAAGTATTTTAAAATTAAAAAAAA
** *
1889364 TTAAAAAAGTATGTAAAAAA-TATTTTAAATTTTAAAAATAAA
1 TTAAAAAA-T-TAAAAAAAAGTATTTTAAA-ATTAAAAA-AAA
1889406 T
1 T
1889407 ATATTTATTA
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
39 12 0.17
40 41 0.58
41 14 0.20
42 4 0.06
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (39 bp):
TTAAAAAATTAAAAAAAAGTATTTTAAAATTAAAAAAAA
Found at i:1896507 original size:44 final size:44
Alignment explanation
Indices: 1896444--1896576 Score: 257
Period size: 44 Copynumber: 3.0 Consensus size: 44
1896434 CATATCTTGG
1896444 TTCTCTGTAAAACAGAATCCTAGTCTCCTAGATGACTTTAATAT
1 TTCTCTGTAAAACAGAATCCTAGTCTCCTAGATGACTTTAATAT
1896488 TTCTCTGTAAAACAGAATCCTAGTCTCCTAGATGACTTTAATAT
1 TTCTCTGTAAAACAGAATCCTAGTCTCCTAGATGACTTTAATAT
*
1896532 TTCTCTGTAAAACAGAATCCTAGTCTCCTAGATAACTTTAATAT
1 TTCTCTGTAAAACAGAATCCTAGTCTCCTAGATGACTTTAATAT
1896576 T
1 T
1896577 CTAACTGGCA
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
44 88 1.00
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (44 bp):
TTCTCTGTAAAACAGAATCCTAGTCTCCTAGATGACTTTAATAT
Found at i:1899157 original size:16 final size:16
Alignment explanation
Indices: 1899136--1899177 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
1899126 TTTAATAGAG
1899136 TCGAGTAAAATGAAAT
1 TCGAGTAAAATGAAAT
** *
1899152 TCGAGTCGAATTAAAT
1 TCGAGTAAAATGAAAT
1899168 T-GAGTAAAAT
1 TCGAGTAAAAT
1899178 TATTTGAATT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.45, C:0.07, G:0.19, T:0.29
Consensus pattern (16 bp):
TCGAGTAAAATGAAAT
Found at i:1899777 original size:2 final size:2
Alignment explanation
Indices: 1899770--1899796 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1899760 TTTCTCTTAA
1899770 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 A
1899797 AAATAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1910370 original size:46 final size:46
Alignment explanation
Indices: 1910303--1910579 Score: 491
Period size: 46 Copynumber: 6.0 Consensus size: 46
1910293 CATGGCAAAG
* ** *
1910303 TGTGAAACGTAGGTATGGTATTTCAATGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAACCATACTGAGT
1910349 TGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAACCATACTGAGT
1910395 TGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAACCATACTGAGT
1910441 TGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAACCATACTGAGT
*
1910487 TGTGAAAAGTAGGTATGGTGTTTCGGTAAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAACCATACTGAGT
* *
1910533 TGTGAAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAACCATACTGAGT
1910579 T
1 T
1910580 ATAGCAATGT
Statistics
Matches: 223, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 223 1.00
ACGTcount: A:0.36, C:0.09, G:0.26, T:0.29
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAACCATACTGAGT
Found at i:1914849 original size:14 final size:14
Alignment explanation
Indices: 1914830--1914880 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
1914820 TTTTCATAAA
*
1914830 TTTATAATTTAATC
1 TTTATAATTTTATC
* *
1914844 TTTATATTTTTATT
1 TTTATAATTTTATC
*
1914858 TTTAAAATTTTA-C
1 TTTATAATTTTATC
1914871 TTT-TAATTTT
1 TTTATAATTTT
1914881 TAAAATTTTA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
12 6 0.20
13 3 0.10
14 21 0.70
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTATAATTTTATC
Found at i:1914874 original size:21 final size:21
Alignment explanation
Indices: 1914850--1914890 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1914840 AATCTTTATA
*
1914850 TTTTTATTTTTAAAATTTTAC
1 TTTTAATTTTTAAAATTTTAC
1914871 TTTTAATTTTTAAAATTTTA
1 TTTTAATTTTTAAAATTTTA
1914891 AAATTTAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTAATTTTTAAAATTTTAC
Found at i:1915073 original size:7 final size:7
Alignment explanation
Indices: 1915061--1915091 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
1915051 ATATCAAAAA
1915061 ATTAAAT
1 ATTAAAT
1915068 ATTAAAT
1 ATTAAAT
1915075 ATTAAAT
1 ATTAAAT
1915082 ATTAAA-
1 ATTAAAT
1915088 ATTA
1 ATTA
1915092 TGATATATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 20 0.83
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
ATTAAAT
Found at i:1915089 original size:22 final size:20
Alignment explanation
Indices: 1915039--1915091 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
1915029 ATAGCTAAAC
1915039 TTAAAATTTAGAATATCAAAAAA
1 TTAAAA-TTA-AATATC-AAAAA
* *
1915062 TTAAATATTAAATATTAAATA
1 TTAAA-ATTAAATATCAAAAA
1915083 TTAAAATTA
1 TTAAAATTA
1915092 TGATATATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 4 0.15
21 9 0.33
22 5 0.19
23 8 0.30
24 1 0.04
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (20 bp):
TTAAAATTAAATATCAAAAA
Found at i:1928960 original size:23 final size:22
Alignment explanation
Indices: 1928907--1928961 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
1928897 TTATGGGTGT
* *
1928907 TGTTTGGTGTTGTAATAGGTGC
1 TGTTTGGTGTTGTAATAGCTAC
*
1928929 TGTCATGGTGTTGTAATAGCTAC
1 TGT-TTGGTGTTGTAATAGCTAC
1928952 TGGTTTGGTG
1 T-GTTTGGTG
1928962 CTGTTTTGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 3 0.11
23 22 0.81
24 2 0.07
ACGTcount: A:0.15, C:0.07, G:0.35, T:0.44
Consensus pattern (22 bp):
TGTTTGGTGTTGTAATAGCTAC
Found at i:1928991 original size:23 final size:23
Alignment explanation
Indices: 1928965--1929020 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
1928955 TTTGGTGCTG
* *
1928965 TTTTGGTGCTGTTATAG-GTGTCA
1 TTTTGGTGCTGCTAT-GTGTGCCA
* *
1928988 TTTTGTTGCTGCTGTGTGTGCCA
1 TTTTGGTGCTGCTATGTGTGCCA
1929011 TTTTGGTGCT
1 TTTTGGTGCT
1929021 ATCAATGCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.07, C:0.12, G:0.30, T:0.50
Consensus pattern (23 bp):
TTTTGGTGCTGCTATGTGTGCCA
Found at i:1930286 original size:42 final size:42
Alignment explanation
Indices: 1930217--1930309 Score: 152
Period size: 42 Copynumber: 2.2 Consensus size: 42
1930207 GTTTTTTTTG
* *
1930217 CAGTTTATGTTCATGATTAATTTTTAGCCTTTCAACAATGTC
1 CAGTCTATGTTCATGATTAATTGTTAGCCTTTCAACAATGTC
1930259 CAGTCTATGTTCATGATTAATTGTTAGCCTTTCAACAATGTC
1 CAGTCTATGTTCATGATTAATTGTTAGCCTTTCAACAATGTC
1930301 C-GCTCTATG
1 CAG-TCTATG
1930310 ATTTGAACTT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
41 1 0.02
42 47 0.98
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (42 bp):
CAGTCTATGTTCATGATTAATTGTTAGCCTTTCAACAATGTC
Found at i:1946995 original size:21 final size:21
Alignment explanation
Indices: 1946963--1947004 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1946953 GCAGTTGAAC
1946963 CACCAAATTGATTAT-TAAAA
1 CACCAAATTGATTATATAAAA
*
1946983 CACCGAATGTGATTATATAAAA
1 CACCAAAT-TGATTATATAAAA
1947005 ATTTAGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 7 0.37
22 5 0.26
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.29
Consensus pattern (21 bp):
CACCAAATTGATTATATAAAA
Found at i:1949303 original size:36 final size:36
Alignment explanation
Indices: 1949214--1949306 Score: 105
Period size: 36 Copynumber: 2.6 Consensus size: 36
1949204 CTCATCAACA
* * * * *
1949214 CCATCTCCGCCGCCGCCACCGAGGAGTCCCGGTACT
1 CCATCTCCACCACCGCCTCCGAGGAATCCCGGGACT
* *
1949250 GCATCTCCACCACCGCCTCCGAGGAATTCCGGGACT
1 CCATCTCCACCACCGCCTCCGAGGAATCCCGGGACT
* *
1949286 CCATCTCCTCCTCCGCCTCCG
1 CCATCTCCACCACCGCCTCCG
1949307 TCTGATTCCA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.14, C:0.48, G:0.20, T:0.17
Consensus pattern (36 bp):
CCATCTCCACCACCGCCTCCGAGGAATCCCGGGACT
Found at i:1979393 original size:7 final size:7
Alignment explanation
Indices: 1979357--1979386 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1979347 GTGCCCTTTC
1979357 TTTTG-T
1 TTTTGTT
1979363 TTTTGTT
1 TTTTGTT
1979370 TTTTGTT
1 TTTTGTT
1979377 TTTTGTT
1 TTTTGTT
1979384 TTT
1 TTT
1979387 ATTTTTTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (7 bp):
TTTTGTT
Found at i:1992511 original size:3 final size:3
Alignment explanation
Indices: 1992503--1992543 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1992493 TTATTTTGCT
1992503 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1992544 GTTCTCACAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1996317 original size:24 final size:23
Alignment explanation
Indices: 1996286--1996332 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 23
1996276 ATAACCACCA
1996286 GACGTGTCAGTACATGTGAGTGT
1 GACGTGTCAGTACATGTGAGTGT
1996309 GACGATGTCAGTACATGTGAGTGT
1 GACG-TGTCAGTACATGTGAGTGT
1996333 AGATAATTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (23 bp):
GACGTGTCAGTACATGTGAGTGT
Found at i:2007849 original size:7 final size:7
Alignment explanation
Indices: 2007837--2007867 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
2007827 CTGATTTGGA
2007837 GAAAATT
1 GAAAATT
2007844 GAAAATT
1 GAAAATT
2007851 GAAAATT
1 GAAAATT
2007858 GAAAA-T
1 GAAAATT
2007864 GAAA
1 GAAA
2007868 CCTGAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (7 bp):
GAAAATT
Found at i:2020734 original size:20 final size:20
Alignment explanation
Indices: 2020709--2020748 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2020699 GCTAAGCACA
2020709 CAACATGATCGACGAAATAC
1 CAACATGATCGACGAAATAC
2020729 CAACATGATCGACGAAATAC
1 CAACATGATCGACGAAATAC
2020749 TCCAAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.25, G:0.15, T:0.15
Consensus pattern (20 bp):
CAACATGATCGACGAAATAC
Found at i:2024508 original size:25 final size:26
Alignment explanation
Indices: 2024458--2024511 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
2024448 TTTTTTAATG
2024458 TTATATTTTGAAATTAAAAAAAAAAC
1 TTATATTTTGAAATTAAAAAAAAAAC
2024484 TTATATTTTGAAATT-AAAAAAAAAC
1 TTATATTTTGAAATTAAAAAAAAAAC
2024509 TTA
1 TTA
2024512 CTTGTTAGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 13 0.46
26 15 0.54
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (26 bp):
TTATATTTTGAAATTAAAAAAAAAAC
Found at i:2024993 original size:3 final size:3
Alignment explanation
Indices: 2024987--2025049 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
2024977 AAGGAAGGAA
2024987 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2025035 ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT
2025050 GTGAACAAAC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2037416 original size:17 final size:15
Alignment explanation
Indices: 2037380--2037409 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2037370 GTTGTAGGCT
*
2037380 TTTATTTTTTGTTAA
1 TTTATTTTTTATTAA
2037395 TTTATTTTTTATTAA
1 TTTATTTTTTATTAA
2037410 AATTTATCAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (15 bp):
TTTATTTTTTATTAA
Found at i:2039707 original size:24 final size:24
Alignment explanation
Indices: 2039680--2039731 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
2039670 TTAGTAGGTC
*
2039680 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* * *
2039704 AAATATATTATACTAATTAATACT
1 AAATAAACTATACTAATAAATACT
2039728 AAAT
1 AAAT
2039732 CTTTTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.35
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:2045754 original size:68 final size:68
Alignment explanation
Indices: 2045630--2045759 Score: 181
Period size: 68 Copynumber: 1.9 Consensus size: 68
2045620 AATTGTTGTA
* *
2045630 TTGAATTAAGGTTGAATCGGCAAAAATAATTATTTAAAGTTTTAAAGTCATATTTCTTAAACATT
1 TTGAATTAAGGTTGAATCGGCAAAAATAATTATTTAAAGGTTTAAAGTCACATTTCTTAAACATT
2045695 AAG
66 AAG
* * * * *
2045698 TTGAATTAAGGTTGAATC-GCTAAATATAATTATTTAAGGGTTTGAAGTTACGTTTCTTAAAC
1 TTGAATTAAGGTTGAATCGGC-AAAAATAATTATTTAAAGGTTTAAAGTCACATTTCTTAAAC
2045760 GTTAGGTTAG
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
67 2 0.04
68 52 0.96
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.39
Consensus pattern (68 bp):
TTGAATTAAGGTTGAATCGGCAAAAATAATTATTTAAAGGTTTAAAGTCACATTTCTTAAACATT
AAG
Found at i:2046656 original size:61 final size:60
Alignment explanation
Indices: 2046522--2046682 Score: 209
Period size: 61 Copynumber: 2.7 Consensus size: 60
2046512 TTTCTACCTG
* * *
2046522 AACTTGACACTTTTTCCTAATTTGGTATCTAAA-CTTTTTTTAGCCCAATTTGGTACTTG
1 AACTTGACACTTTTTCCTAATTTGGTACCTAAACCTTTTTTTAGCCCAATTTGGTACGTC
* * * *
2046581 AACTTGACACTTTTTTCTAATTTGGCACCTAAACCATTTTTTTGGCCCAATTTTGTACGTC
1 AACTTGACACTTTTTCCTAATTTGGTACCTAAACC-TTTTTTTAGCCCAATTTGGTACGTC
* * *
2046642 AACTTGGCATTTTTTCCTAATTTAGTACCT-AACCTTTTTTT
1 AACTTGACACTTTTTCCTAATTTGGTACCTAAACCTTTTTTT
2046683 TAGGTTCATT
Statistics
Matches: 88, Mismatches: 12, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
59 37 0.42
60 5 0.06
61 46 0.52
ACGTcount: A:0.23, C:0.20, G:0.11, T:0.46
Consensus pattern (60 bp):
AACTTGACACTTTTTCCTAATTTGGTACCTAAACCTTTTTTTAGCCCAATTTGGTACGTC
Found at i:2047174 original size:31 final size:32
Alignment explanation
Indices: 2047136--2047209 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 32
2047126 TAGACCCAAA
* *
2047136 AAATTTAAGTACT-AATTTAA-AAAAATATATT
1 AAATTTAAGTACTCAAATTAAGAAAAA-ATATC
2047167 AAATTTAAGTA-TCAAATTAAGAAAAAATATC
1 AAATTTAAGTACTCAAATTAAGAAAAAATATC
*
2047198 AAGTTTAAGTAC
1 AAATTTAAGTAC
2047210 AGGTTAGAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
30 1 0.03
31 31 0.84
32 5 0.14
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.34
Consensus pattern (32 bp):
AAATTTAAGTACTCAAATTAAGAAAAAATATC
Found at i:2052401 original size:18 final size:18
Alignment explanation
Indices: 2052368--2052402 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2052358 TCATCAATGG
* *
2052368 CGTCATCACCTTCCTCAT
1 CGTCATCAACTACCTCAT
2052386 CGTCATCAACTACCTCA
1 CGTCATCAACTACCTCA
2052403 GCTTCTTATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.43, G:0.06, T:0.29
Consensus pattern (18 bp):
CGTCATCAACTACCTCAT
Found at i:2071646 original size:13 final size:13
Alignment explanation
Indices: 2071628--2071654 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2071618 GCAAGTAGAC
2071628 TATGGTTCAAGCT
1 TATGGTTCAAGCT
2071641 TATGGTTCAAGCT
1 TATGGTTCAAGCT
2071654 T
1 T
2071655 CTTTCATGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.41
Consensus pattern (13 bp):
TATGGTTCAAGCT
Found at i:2072024 original size:20 final size:20
Alignment explanation
Indices: 2071999--2072038 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2071989 AATTTTTGTG
2071999 TAAAACTAAAAGGAAAATAC
1 TAAAACTAAAAGGAAAATAC
2072019 TAAAACTAAAAGGAAAATAC
1 TAAAACTAAAAGGAAAATAC
2072039 ACTATCTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.65, C:0.10, G:0.10, T:0.15
Consensus pattern (20 bp):
TAAAACTAAAAGGAAAATAC
Found at i:2075114 original size:2 final size:2
Alignment explanation
Indices: 2075107--2075143 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
2075097 TAATCTTACT
*
2075107 TA TA TA TA TA TA TA TA TA TA TT TA TA T- TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2075144 TTGCTTGGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:2089158 original size:3 final size:3
Alignment explanation
Indices: 2089150--2089209 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
2089140 CAGTGATCCA
2089150 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2089198 AAT AAT AAT AAT
1 AAT AAT AAT AAT
2089210 GCAGTCAGGT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2092112 original size:11 final size:11
Alignment explanation
Indices: 2092091--2092119 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2092081 GTCTCTTTCT
2092091 TCTCTCT-CCC
1 TCTCTCTCCCC
2092101 TCTCTCTCCCC
1 TCTCTCTCCCC
2092112 TCTCTCTC
1 TCTCTCTC
2092120 TCCCCGTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (11 bp):
TCTCTCTCCCC
Found at i:2092183 original size:3 final size:3
Alignment explanation
Indices: 2092175--2092201 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2092165 GGAAAAGATC
2092175 AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA
2092202 CGGCGACGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2096267 original size:9 final size:9
Alignment explanation
Indices: 2096242--2096271 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
2096232 ATCATTAGCC
2096242 TAAGTTAAT
1 TAAGTTAAT
2096251 TAAGGTTAAT
1 TAA-GTTAAT
2096261 TAAGTTAAT
1 TAAGTTAAT
2096270 TA
1 TA
2096272 TGATTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (9 bp):
TAAGTTAAT
Found at i:2096281 original size:19 final size:19
Alignment explanation
Indices: 2096242--2096281 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2096232 ATCATTAGCC
*
2096242 TAAGTTAATTAAGGTTAAT
1 TAAGTTAATTAAGATTAAT
* *
2096261 TAAGTTAATTATGATTTAT
1 TAAGTTAATTAAGATTAAT
2096280 TA
1 TA
2096282 TATATTAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.47
Consensus pattern (19 bp):
TAAGTTAATTAAGATTAAT
Found at i:2104166 original size:30 final size:31
Alignment explanation
Indices: 2104105--2104166 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
2104095 AATTTTTTAA
*
2104105 ATTTTTAAAAATTCAAAAAATAATAATATAT
1 ATTTTTAAAAATTCAAAAAATAATAAAATAT
* *
2104136 ATTTTTAAAAATT-AAAAATTATTAAAATAT
1 ATTTTTAAAAATTCAAAAAATAATAAAATAT
2104166 A
1 A
2104167 AACAATATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 15 0.54
31 13 0.46
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (31 bp):
ATTTTTAAAAATTCAAAAAATAATAAAATAT
Found at i:2114464 original size:3 final size:3
Alignment explanation
Indices: 2114456--2114480 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2114446 GGAAAAAATG
2114456 TAC TAC TAC TAC TAC TAC TAC TAC T
1 TAC TAC TAC TAC TAC TAC TAC TAC T
2114481 TTATAGAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TAC
Found at i:2117761 original size:22 final size:20
Alignment explanation
Indices: 2117727--2117771 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
2117717 ATAGTAATTC
2117727 TATTTTTTCTTCAACAGAAAA
1 TATTTTTTCTTCAACA-AAAA
* *
2117748 TATTTTTTATTTCAATAAAAA
1 TATTTTTT-CTTCAACAAAAA
2117769 TAT
1 TAT
2117772 ATATCATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (20 bp):
TATTTTTTCTTCAACAAAAA
Found at i:2121491 original size:45 final size:46
Alignment explanation
Indices: 2121442--2121535 Score: 147
Period size: 45 Copynumber: 2.1 Consensus size: 46
2121432 TAAATAACAT
* *
2121442 AAAATTGCATAACTTAGTGAATTCTGTTCTAATA-ATT-AAAGATTA
1 AAAATTGCATAACTTAGTGAATTCTGGTCTAA-AGATTAAAAGAGTA
2121487 AAAATTGCATAACTTAGTGAATTCTGGTCTAAAGATTAAAAGAGTA
1 AAAATTGCATAACTTAGTGAATTCTGGTCTAAAGATTAAAAGAGTA
2121533 AAA
1 AAA
2121536 TGAATAAATG
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
44 1 0.02
45 34 0.76
46 10 0.22
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.33
Consensus pattern (46 bp):
AAAATTGCATAACTTAGTGAATTCTGGTCTAAAGATTAAAAGAGTA
Found at i:2126449 original size:21 final size:21
Alignment explanation
Indices: 2126423--2126477 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
2126413 ATAATAGTGG
*
2126423 CGGTGAGATTAGTTACTGTAA
1 CGGTGAGATTAGATACTGTAA
* *
2126444 CGGTGAGATTGGATACTGTAG
1 CGGTGAGATTAGATACTGTAA
2126465 CGGTGAGATTAGA
1 CGGTGAGATTAGA
2126478 AACAATGGTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.27, C:0.09, G:0.35, T:0.29
Consensus pattern (21 bp):
CGGTGAGATTAGATACTGTAA
Found at i:2140242 original size:27 final size:27
Alignment explanation
Indices: 2140212--2140263 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
2140202 CAATTTTTTA
2140212 ATTATTAATAATTATAAATTTAATATT
1 ATTATTAATAATTATAAATTTAATATT
** * *
2140239 ATTATTTTTAATTGTTAATTTAATA
1 ATTATTAATAATTATAAATTTAATA
2140264 ATATGTTATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (27 bp):
ATTATTAATAATTATAAATTTAATATT
Found at i:2140265 original size:15 final size:15
Alignment explanation
Indices: 2140216--2140265 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 15
2140206 TTTTTAATTA
*
2140216 TTAATAATTATAAAT
1 TTAATAATTATTAAT
2140231 TTAAT-ATTATT-AT
1 TTAATAATTATTAAT
* *
2140244 TT-TTAATTGTTAAT
1 TTAATAATTATTAAT
2140258 TTAATAAT
1 TTAATAAT
2140266 ATGTTATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
12 1 0.04
13 9 0.32
14 9 0.32
15 9 0.32
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
TTAATAATTATTAAT
Found at i:2140354 original size:7 final size:7
Alignment explanation
Indices: 2140344--2140376 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
2140334 ATTATAAATA
2140344 TAGATTG
1 TAGATTG
2140351 TAGATTG
1 TAGATTG
2140358 TAGATTG
1 TAGATTG
2140365 TAGATTG
1 TAGATTG
2140372 TAGAT
1 TAGAT
2140377 AATAACAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.30, C:0.00, G:0.27, T:0.42
Consensus pattern (7 bp):
TAGATTG
Found at i:2140807 original size:8 final size:8
Alignment explanation
Indices: 2140794--2140827 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
2140784 AAAATATTTT
2140794 AAAATTAA
1 AAAATTAA
*
2140802 AAAATTTA
1 AAAATTAA
2140810 AAAATT-A
1 AAAATTAA
2140817 AAAATTAA
1 AAAATTAA
2140825 AAA
1 AAA
2140828 GAGTATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 7 0.29
8 17 0.71
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
AAAATTAA
Found at i:2140808 original size:16 final size:17
Alignment explanation
Indices: 2140781--2140821 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 17
2140771 AAAAAGTATT
*
2140781 TTAAAAATATTTTAAAA
1 TTAAAAATATTTAAAAA
2140798 TTAAAAA-ATTTAAAAA
1 TTAAAAATATTTAAAAA
2140814 TTAAAAAT
1 TTAAAAAT
2140822 TAAAAAGAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TTAAAAATATTTAAAAA
Found at i:2140827 original size:7 final size:7
Alignment explanation
Indices: 2140794--2140827 Score: 50
Period size: 7 Copynumber: 4.6 Consensus size: 7
2140784 AAAATATTTT
2140794 AAAATTAA
1 AAAATT-A
2140802 AAAATTTA
1 AAAA-TTA
2140810 AAAATTA
1 AAAATTA
2140817 AAAATTA
1 AAAATTA
2140824 AAAA
1 AAAA
2140828 GAGTATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 14 0.56
8 9 0.36
9 2 0.08
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AAAATTA
Found at i:2140839 original size:54 final size:51
Alignment explanation
Indices: 2140751--2140858 Score: 171
Period size: 54 Copynumber: 2.1 Consensus size: 51
2140741 ATTTTATTTT
2140751 AAAATTTAAAACAAAAATTAAAAAAGTATTTTAAAAATATTTTAAAATTAA
1 AAAATTTAAAACAAAAATTAAAAAAGTATTTTAAAAATATTTTAAAATTAA
* *
2140802 AAAATTTAAAAATTAAAAATTAAAAAGAGTATTTTAAAAGTATTTTAAAATTAA
1 AAAATTT-AAAA-CAAAAATTAAAAA-AGTATTTTAAAAATATTTTAAAATTAA
2140856 AAA
1 AAA
2140859 TAAAATATTT
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
51 7 0.13
52 4 0.08
53 12 0.23
54 29 0.56
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (51 bp):
AAAATTTAAAACAAAAATTAAAAAAGTATTTTAAAAATATTTTAAAATTAA
Found at i:2144963 original size:68 final size:68
Alignment explanation
Indices: 2144854--2144990 Score: 274
Period size: 68 Copynumber: 2.0 Consensus size: 68
2144844 GTTCACACAT
2144854 TCCTCTGTTTTGCTTTTATGTCATCGACTTTCTTTCCTGAATAGTATTCCTTTTGGATTTGGCTT
1 TCCTCTGTTTTGCTTTTATGTCATCGACTTTCTTTCCTGAATAGTATTCCTTTTGGATTTGGCTT
2144919 TGC
66 TGC
2144922 TCCTCTGTTTTGCTTTTATGTCATCGACTTTCTTTCCTGAATAGTATTCCTTTTGGATTTGGCTT
1 TCCTCTGTTTTGCTTTTATGTCATCGACTTTCTTTCCTGAATAGTATTCCTTTTGGATTTGGCTT
2144987 TGC
66 TGC
2144990 T
1 T
2144991 TGTTGTGGCT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.12, C:0.20, G:0.16, T:0.52
Consensus pattern (68 bp):
TCCTCTGTTTTGCTTTTATGTCATCGACTTTCTTTCCTGAATAGTATTCCTTTTGGATTTGGCTT
TGC
Found at i:2146365 original size:7 final size:7
Alignment explanation
Indices: 2146353--2146381 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
2146343 AAAAGTAAGT
2146353 AATGTCA
1 AATGTCA
2146360 AATGTCA
1 AATGTCA
2146367 AATGTCA
1 AATGTCA
2146374 AATGTCA
1 AATGTCA
2146381 A
1 A
2146382 TCTCTATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.28
Consensus pattern (7 bp):
AATGTCA
Found at i:2151040 original size:2 final size:2
Alignment explanation
Indices: 2151033--2151058 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2151023 ATAAATGAAC
2151033 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
2151059 TTGCAAAAAT
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):
AT
Found at i:2155102 original size:23 final size:24
Alignment explanation
Indices: 2155054--2155111 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
2155044 AACAAATTAC
* *
2155054 TAATAAAATAA-TAAAATATCATT
1 TAATAAACTAATTAAAATATCAAT
* *
2155077 TAA-AATCTAATTAAAATATTAAT
1 TAATAAACTAATTAAAATATCAAT
2155100 TAATAAACTAAT
1 TAATAAACTAAT
2155112 ATTTATTTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
22 5 0.18
23 16 0.57
24 7 0.25
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (24 bp):
TAATAAACTAATTAAAATATCAAT
Found at i:2157308 original size:51 final size:51
Alignment explanation
Indices: 2157249--2157408 Score: 166
Period size: 51 Copynumber: 3.2 Consensus size: 51
2157239 GTTCACATAA
* *
2157249 TAGCCTGCACATAGTACTACACATGTGA-CCATTACCATCCGATACATGTAG
1 TAGCCTGCACATAGTACTACACATGTGACCCA-TACCATCCGGTACACGTAG
* * * * * * *
2157300 TAGCCTGCATATAGTACTACAC-TCGTGATCGAAACTATCCGGTACGCATAG
1 TAGCCTGCACATAGTACTACACAT-GTGACCCATACCATCCGGTACACGTAG
* *
2157351 TAGCCTGCATATAGTACTACACATGCGACCCAT--CATTCCGGTACACGTAG
1 TAGCCTGCACATAGTACTACACATGTGACCCATACCA-TCCGGTACACGTAG
2157401 TAGCCTGC
1 TAGCCTGC
2157409 TAGTACGACA
Statistics
Matches: 90, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
49 1 0.01
50 21 0.23
51 65 0.72
52 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (51 bp):
TAGCCTGCACATAGTACTACACATGTGACCCATACCATCCGGTACACGTAG
Found at i:2182093 original size:29 final size:29
Alignment explanation
Indices: 2182057--2182123 Score: 116
Period size: 29 Copynumber: 2.3 Consensus size: 29
2182047 CACTTGGAAC
2182057 ATGTAAGAAATCCATTTGCATTAAACAAA
1 ATGTAAGAAATCCATTTGCATTAAACAAA
* *
2182086 ATGTAAGAAATCTATTTGTATTAAACAAA
1 ATGTAAGAAATCCATTTGCATTAAACAAA
2182115 ATGTAAGAA
1 ATGTAAGAA
2182124 TGCATGTGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.30
Consensus pattern (29 bp):
ATGTAAGAAATCCATTTGCATTAAACAAA
Found at i:2188875 original size:31 final size:31
Alignment explanation
Indices: 2188839--2188913 Score: 77
Period size: 30 Copynumber: 2.5 Consensus size: 31
2188829 ATTAATAGTT
*
2188839 TATAAAAATTGA-ATCAAATCAAAATTT-TGTA
1 TATAAAAATT-ACATAAAATCAAAATTTAT-TA
*
2188870 TAT-AAAATTACATAAAATTAAAATTTATTA
1 TATAAAAATTACATAAAATCAAAATTTATTA
*
2188900 GATAAAAATT-CATA
1 TATAAAAATTACATA
2188914 TATAATTTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
29 1 0.03
30 27 0.71
31 10 0.26
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.36
Consensus pattern (31 bp):
TATAAAAATTACATAAAATCAAAATTTATTA
Found at i:2189654 original size:81 final size:81
Alignment explanation
Indices: 2189519--2189685 Score: 289
Period size: 81 Copynumber: 2.1 Consensus size: 81
2189509 TTCTACTATT
* * *
2189519 AGAAAAAGATAAGAATGACTTGAAATCACAGTTTTATACAATTTTTTCTCTTAGTAACTTGAGTT
1 AGAAAAAGATAAGAATGACGTAAAATCACAGTTTCATACAATTTTTTCTCTTAGTAACTTGAGTT
2189584 TCTAAATAACCAACCG
66 TCTAAATAACCAACCG
* *
2189600 AGAAAAAGATAAGAGTGACGTAAAATCATAGTTTCATACAATTTTTTCTCTTAGTAACTTGAGTT
1 AGAAAAAGATAAGAATGACGTAAAATCACAGTTTCATACAATTTTTTCTCTTAGTAACTTGAGTT
2189665 TCTAAATAACCAACCG
66 TCTAAATAACCAACCG
2189681 AGAAA
1 AGAAA
2189686 TTAGGAACAG
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (81 bp):
AGAAAAAGATAAGAATGACGTAAAATCACAGTTTCATACAATTTTTTCTCTTAGTAACTTGAGTT
TCTAAATAACCAACCG
Found at i:2191559 original size:13 final size:13
Alignment explanation
Indices: 2191541--2191565 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2191531 ATGGAAGAAA
2191541 AAAAATAAAAGGT
1 AAAAATAAAAGGT
2191554 AAAAATAAAAGG
1 AAAAATAAAAGG
2191566 GATAAGGTTT
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:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (13 bp):
AAAAATAAAAGGT
Found at i:2194673 original size:5 final size:5
Alignment explanation
Indices: 2194665--2194690 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2194655 TTAGATTAGT
2194665 TGACC TGACC TGACC TGACC TGACC T
1 TGACC TGACC TGACC TGACC TGACC T
2194691 TTAGCATTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.38, G:0.19, T:0.23
Consensus pattern (5 bp):
TGACC
Found at i:2195962 original size:2 final size:2
Alignment explanation
Indices: 2195957--2195989 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2195947 TTTTATCTTT
*
2195957 TG TG TG AG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
2195990 TTCAACACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.03, C:0.00, G:0.48, T:0.48
Consensus pattern (2 bp):
TG
Found at i:2202003 original size:24 final size:23
Alignment explanation
Indices: 2201957--2202004 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
2201947 ATTTATATTG
2201957 TTTATTTTAAATTTATTGAATAA
1 TTTATTTTAAATTTATTGAATAA
* * *
2201980 TTTATTGTTATATTTTTTGCATAA
1 TTTATT-TTAAATTTATTGAATAA
2202004 T
1 T
2202005 AAAACTTTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.60
Consensus pattern (23 bp):
TTTATTTTAAATTTATTGAATAA
Found at i:2209512 original size:23 final size:22
Alignment explanation
Indices: 2209473--2209515 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
2209463 ATAATTTATC
2209473 AAAAAAAATAACTTTTTAAAGT
1 AAAAAAAATAACTTTTTAAAGT
2209495 AAAACAAAATAA-TATTTTAAA
1 AAAA-AAAATAACT-TTTTAAA
2209516 ATTTAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (22 bp):
AAAAAAAATAACTTTTTAAAGT
Found at i:2215547 original size:2 final size:2
Alignment explanation
Indices: 2215505--2215535 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2215495 TTTTTTCCCC
2215505 AT 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 AT A
2215536 ACAGGTTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2218372 original size:19 final size:19
Alignment explanation
Indices: 2218348--2218405 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
2218338 AATTATTTAT
2218348 TAAATT-TAATTAGAATATA
1 TAAATTATAATTA-AATATA
* *
2218367 TAAATTATATTTAAATATT
1 TAAATTATAATTAAATATA
*
2218386 TAAATACAATAATTAAATAT
1 TAAAT--TATAATTAAATAT
2218406 TTGTAATTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 16 0.50
20 5 0.16
21 11 0.34
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
TAAATTATAATTAAATATA
Found at i:2220302 original size:72 final size:72
Alignment explanation
Indices: 2220163--2220396 Score: 375
Period size: 72 Copynumber: 3.3 Consensus size: 72
2220153 AAAATCATAT
* *
2220163 ATAAACAACTATTGATAAAATTA-ATT-TAGTATAAATAAGTAGAAC-TAAATTCAATATCCAAA
1 ATAAACAACTATTGATAAAACTAGATTATA-CATAAATAAGTAGAACATAAATTCAATATCCAAA
*
2220225 GACCAAAC
65 AACCAAAC
*
2220233 ATAAACAACTATTAATAAAACTAGATTATACATAAATAAGTAGAACATAAATTCAATATCCAAAA
1 ATAAACAACTATTGATAAAACTAGATTATACATAAATAAGTAGAACATAAATTCAATATCCAAAA
2220298 ACCAAAC
66 ACCAAAC
* *
2220305 ATAAACAACCATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATCCAAAA
1 ATAAACAACTATTGATAAAACTAGATTATACATAAATAAGTAGAACATAAATTCAATATCCAAAA
2220370 ACCAAAC
66 ACCAAAC
*
2220377 ATAAATAACTATTGATAAAA
1 ATAAACAACTATTGATAAAA
2220397 AACTAGTTTA
Statistics
Matches: 152, Mismatches: 9, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
70 21 0.14
71 18 0.12
72 113 0.74
ACGTcount: A:0.56, C:0.15, G:0.06, T:0.24
Consensus pattern (72 bp):
ATAAACAACTATTGATAAAACTAGATTATACATAAATAAGTAGAACATAAATTCAATATCCAAAA
ACCAAAC
Found at i:2220852 original size:18 final size:18
Alignment explanation
Indices: 2220831--2220878 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
2220821 TCCATCAATT
*
2220831 TGAACATCATTTGAAATG
1 TGAACATCATTTAAAATG
2220849 TGAACATCATTTAAAATG
1 TGAACATCATTTAAAATG
2220867 TGAACATCATTT
1 TGAACATCATTT
2220879 CTCATATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (18 bp):
TGAACATCATTTAAAATG
Found at i:2223749 original size:16 final size:16
Alignment explanation
Indices: 2223728--2223759 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2223718 ACATGACAGG
2223728 GTTTTAATATCTCTTT
1 GTTTTAATATCTCTTT
*
2223744 GTTTTAGTATCTCTTT
1 GTTTTAATATCTCTTT
2223760 CATTTTTGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.12, G:0.09, T:0.62
Consensus pattern (16 bp):
GTTTTAATATCTCTTT
Found at i:2249903 original size:52 final size:52
Alignment explanation
Indices: 2249826--2249979 Score: 254
Period size: 52 Copynumber: 3.0 Consensus size: 52
2249816 ATAGGGGATA
*
2249826 AAAGCTAAACGAGCAGATAAAAGGGAATCTGCTTTTACAAAATGAAAGACAT
1 AAAGCTAAACGAGCAGATAAAAGGGAATCTGCTTTTACAAAGTGAAAGACAT
* *
2249878 AAAGCTAAATGAGCAGATAAGAGGGAATCTGCTTTTACAAAGTGAAAGACAT
1 AAAGCTAAACGAGCAGATAAAAGGGAATCTGCTTTTACAAAGTGAAAGACAT
* * *
2249930 AAAGCCAAACGAGCAGATAAAAGGGGATCTACTTTTACAAAGTGAAAGAC
1 AAAGCTAAACGAGCAGATAAAAGGGAATCTGCTTTTACAAAGTGAAAGAC
2249980 GATTATTCAT
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 94 1.00
ACGTcount: A:0.46, C:0.14, G:0.21, T:0.19
Consensus pattern (52 bp):
AAAGCTAAACGAGCAGATAAAAGGGAATCTGCTTTTACAAAGTGAAAGACAT
Found at i:2256252 original size:42 final size:42
Alignment explanation
Indices: 2256188--2256282 Score: 172
Period size: 42 Copynumber: 2.2 Consensus size: 42
2256178 TTACTGATAT
*
2256188 TCATAAACATGGTGGAATAATCTTTGAGACATCATGAGGTGG
1 TCATAAACATGGTGGAACAATCTTTGAGACATCATGAGGTGG
2256230 TCATAAACATGGTGGAACAATCTTTGAGACATCATGAGGTGG
1 TCATAAACATGGTGGAACAATCTTTGAGACATCATGAGGTGG
2256272 TCATAATACAT
1 TCATAA-ACAT
2256283 CAAAAATTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 47 0.92
43 4 0.08
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (42 bp):
TCATAAACATGGTGGAACAATCTTTGAGACATCATGAGGTGG
Found at i:2264761 original size:16 final size:18
Alignment explanation
Indices: 2264732--2264767 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
2264722 CAGAATATAT
2264732 TTATTTTAATAAATATTA
1 TTATTTTAATAAATATTA
2264750 TTATTTT-A-AAATATTA
1 TTATTTTAATAAATATTA
2264766 TT
1 TT
2264768 TTACACCCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 1 0.06
18 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTATTTTAATAAATATTA
Found at i:2280180 original size:70 final size:72
Alignment explanation
Indices: 2280048--2280184 Score: 233
Period size: 70 Copynumber: 1.9 Consensus size: 72
2280038 ATCCATAAAG
*
2280048 GGCGATTAAAATCAATTCATGAAACAGTAAAAGAAAGTAATTTTACACACTTTTGAGATTCAATG
1 GGCGATTAAAATCAATTAATGAAACAGTAAAAGAAAGTAATTTTACACACTTTTGAGATTCAATG
2280113 ATAAAAA
66 ATAAAAA
* *
2280120 GGCGTTTAAAATCACTTAATGAAACAGT-AAAGAAAGTAA-TTTACACACTTTTGAGATTCAATG
1 GGCGATTAAAATCAATTAATGAAACAGTAAAAGAAAGTAATTTTACACACTTTTGAGATTCAATG
2280183 AT
66 AT
2280185 CGGCATACGT
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
70 26 0.42
71 11 0.18
72 25 0.40
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.29
Consensus pattern (72 bp):
GGCGATTAAAATCAATTAATGAAACAGTAAAAGAAAGTAATTTTACACACTTTTGAGATTCAATG
ATAAAAA
Found at i:2281139 original size:23 final size:23
Alignment explanation
Indices: 2281104--2281149 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2281094 CCTCTCCATA
*
2281104 GGGTAGAACTTTTCTTT-TCTTTT
1 GGGTAGAAATTTT-TTTATCTTTT
*
2281127 GGGTATAAATTTTTTTATCTTTT
1 GGGTAGAAATTTTTTTATCTTTT
2281150 TAGCGAGGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.17, C:0.09, G:0.15, T:0.59
Consensus pattern (23 bp):
GGGTAGAAATTTTTTTATCTTTT
Found at i:2281400 original size:11 final size:11
Alignment explanation
Indices: 2281355--2281403 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
2281345 TATTTTTTAA
*
2281355 TTTTAAAATAC
1 TTTTAAAATAT
2281366 TTTTAAAATAT
1 TTTTAAAATAT
***
2281377 TTTTATTTTTAT
1 TTTTA-AAATAT
2281389 TTTTAAAATAT
1 TTTTAAAATAT
2281400 TTTT
1 TTTT
2281404 TGTATTTATT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
11 22 0.73
12 8 0.27
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:2281737 original size:19 final size:19
Alignment explanation
Indices: 2281713--2281777 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 19
2281703 TTTTACTTTT
2281713 TTTATTGTAATATGTACAA
1 TTTATTGTAATATGTACAA
* *
2281732 TTTA-T-T-ATCTTTATCAA
1 TTTATTGTAATATGTA-CAA
*
2281749 TTTTTATTGTAATATGCACAA
1 --TTTATTGTAATATGTACAA
2281770 TTTATTGT
1 TTTATTGT
2281778 CTTCTTCAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 12
0.67 0.10 0.23
Matches are distributed among these distances:
16 5 0.14
17 4 0.11
18 1 0.03
19 16 0.46
20 1 0.03
21 4 0.11
22 4 0.11
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (19 bp):
TTTATTGTAATATGTACAA
Found at i:2281759 original size:38 final size:38
Alignment explanation
Indices: 2281711--2281788 Score: 122
Period size: 38 Copynumber: 2.1 Consensus size: 38
2281701 TTTTTTACTT
*
2281711 TTTTTATTGTAATATGTACAATTTATTATCTT-TATCAA
1 TTTTTATTGTAATATGCACAATTTATTATCTTCT-TCAA
*
2281749 TTTTTATTGTAATATGCACAATTTATTGTCTTCTTCAA
1 TTTTTATTGTAATATGCACAATTTATTATCTTCTTCAA
2281787 TT
1 TT
2281789 GCATATCTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 36 0.97
39 1 0.03
ACGTcount: A:0.28, C:0.10, G:0.06, T:0.55
Consensus pattern (38 bp):
TTTTTATTGTAATATGCACAATTTATTATCTTCTTCAA
Found at i:2283604 original size:18 final size:18
Alignment explanation
Indices: 2283581--2283617 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2283571 TTCAATTGTC
2283581 ACTTCAATTGATTTTTTT
1 ACTTCAATTGATTTTTTT
2283599 ACTTCAATTGATTTTTTT
1 ACTTCAATTGATTTTTTT
2283617 A
1 A
2283618 GTCTCGTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.11, G:0.05, T:0.59
Consensus pattern (18 bp):
ACTTCAATTGATTTTTTT
Found at i:2298683 original size:2 final size:2
Alignment explanation
Indices: 2298676--2298718 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2298666 ATTCATCTAC
2298676 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
2298718 T
1 T
2298719 TCGTATTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2299833 original size:23 final size:23
Alignment explanation
Indices: 2299801--2299844 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2299791 ACTACCATTT
2299801 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
2299824 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
2299845 ACAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:2300957 original size:29 final size:30
Alignment explanation
Indices: 2300893--2300958 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
2300883 AAAAATAAAA
*
2300893 ATTATATATAAATTTTGATTTAATGTGCAAT
1 ATTATATATAAACTTTGATTTAATGT-CAAT
* *
2300924 ATTATATATGAACTTTGATTTTATGT-AAT
1 ATTATATATAAACTTTGATTTAATGTCAAT
*
2300953 TTTATA
1 ATTATA
2300959 CATAGAATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 8 0.26
31 23 0.74
ACGTcount: A:0.36, C:0.03, G:0.09, T:0.52
Consensus pattern (30 bp):
ATTATATATAAACTTTGATTTAATGTCAAT
Found at i:2314505 original size:21 final size:21
Alignment explanation
Indices: 2314465--2314509 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
2314455 TTTTAAAAAC
2314465 AATTAATAATCATTATTTTTAA
1 AATTAATAATCA-TATTTTTAA
2314487 AATTAAATAATCA-ATTTTTAA
1 AATT-AATAATCATATTTTTAA
2314508 AA
1 AA
2314510 AAATTAGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.45
22 4 0.18
23 8 0.36
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (21 bp):
AATTAATAATCATATTTTTAA
Found at i:2314505 original size:22 final size:22
Alignment explanation
Indices: 2314465--2314510 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2314455 TTTTAAAAAC
* *
2314465 AATTAATAATCATTATTTTTAA
1 AATTAATAATCAATATTTTAAA
2314487 AATTAAATAATCAAT-TTTTAAA
1 AATT-AATAATCAATATTTTAAA
2314509 AA
1 AA
2314511 AATTAGATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (22 bp):
AATTAATAATCAATATTTTAAA
Found at i:2314520 original size:24 final size:24
Alignment explanation
Indices: 2314455--2314520 Score: 68
Period size: 23 Copynumber: 2.8 Consensus size: 24
2314445 CTTTAAAAAA
2314455 TTTTAAAAACAATTAATAATCATTAT
1 TTTTAAAAA-AATTAATAATCA-TAT
2314481 TTTT---AAAATTAAATAATCA-AT
1 TTTTAAAAAAATT-AATAATCATAT
2314502 TTTTAAAAAAATTAGATAA
1 TTTTAAAAAAATTA-ATAA
2314521 ATATTTAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
21 6 0.17
22 4 0.11
23 11 0.31
24 10 0.29
26 4 0.11
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.41
Consensus pattern (24 bp):
TTTTAAAAAAATTAATAATCATAT
Found at i:2314522 original size:28 final size:29
Alignment explanation
Indices: 2314490--2314563 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
2314480 TTTTTAAAAT
* *
2314490 TAAATAATCAATTTTTAAAAA-AATTAGA
1 TAAATAATAAATTTTAAAAAACAATTAGA
* * *
2314518 TAAATATTTAATTAATAAAAAACAATTAGA
1 TAAATAATAAATT-TTAAAAAACAATTAGA
2314548 T-AATAATAAATTTTAA
1 TAAATAATAAATTTTAA
2314564 GTATATATTA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
28 14 0.38
29 15 0.41
30 8 0.22
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (29 bp):
TAAATAATAAATTTTAAAAAACAATTAGA
Found at i:2314653 original size:17 final size:18
Alignment explanation
Indices: 2314633--2314667 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
2314623 ATCATAAATC
2314633 AATCATAATTA-TCTTTT
1 AATCATAATTACTCTTTT
2314650 AATCATAATTACTCTTTT
1 AATCATAATTACTCTTTT
2314668 GTAACTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.51
Consensus pattern (18 bp):
AATCATAATTACTCTTTT
Found at i:2321310 original size:30 final size:30
Alignment explanation
Indices: 2321274--2321336 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
2321264 ATCCTGCATG
2321274 ATAGAGGTGGCATTTAATGAAATAAATAGA
1 ATAGAGGTGGCATTTAATGAAATAAATAGA
* *
2321304 ATAGAGGTGGCGTTTAATGAAATAAATCGA
1 ATAGAGGTGGCATTTAATGAAATAAATAGA
2321334 ATA
1 ATA
2321337 AAAGAATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.44, C:0.05, G:0.24, T:0.27
Consensus pattern (30 bp):
ATAGAGGTGGCATTTAATGAAATAAATAGA
Found at i:2338679 original size:10 final size:12
Alignment explanation
Indices: 2338660--2338691 Score: 50
Period size: 10 Copynumber: 2.8 Consensus size: 12
2338650 CCATTCAATT
2338660 TAATTATTTAAA
1 TAATTATTTAAA
2338672 -AA-TATTTAAA
1 TAATTATTTAAA
2338682 TAATTATTTA
1 TAATTATTTA
2338692 TTTTTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
10 8 0.44
11 4 0.22
12 6 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TAATTATTTAAA
Found at i:2357511 original size:10 final size:10
Alignment explanation
Indices: 2357496--2357600 Score: 52
Period size: 10 Copynumber: 10.3 Consensus size: 10
2357486 CCTTTGTATG
*
2357496 TTTTTAGATT
1 TTTTTAAATT
2357506 TTTTTAAATT
1 TTTTTAAATT
* *
2357516 TTTATATATT
1 TTTTTAAATT
*
2357526 TTTAAATACAATT
1 TTT--TTA-AATT
2357539 TTTTTAAATT
1 TTTTTAAATT
* *
2357549 TCTATAAA-T
1 TTTTTAAATT
* *
2357558 ATTTTGAATT
1 TTTTTAAATT
**
2357568 TTTAAAAATT
1 TTTTTAAATT
* *
2357578 ATTTT-GATT
1 TTTTTAAATT
2357587 TTTTTATAATT
1 TTTTTA-AATT
2357598 TTT
1 TTT
2357601 GTTTAGAGAG
Statistics
Matches: 68, Mismatches: 21, Indels: 11
0.68 0.21 0.11
Matches are distributed among these distances:
9 12 0.18
10 39 0.57
11 8 0.12
12 3 0.04
13 6 0.09
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (10 bp):
TTTTTAAATT
Found at i:2357519 original size:18 final size:18
Alignment explanation
Indices: 2357496--2357532 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2357486 CCTTTGTATG
*
2357496 TTTTTAGATTTTTTTAAA
1 TTTTTAGATATTTTTAAA
*
2357514 TTTTTATATATTTTTAAA
1 TTTTTAGATATTTTTAAA
2357532 T
1 T
2357533 ACAATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTTTAGATATTTTTAAA
Found at i:2357549 original size:23 final size:25
Alignment explanation
Indices: 2357512--2357558 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
2357502 GATTTTTTTA
*
2357512 AATTTTTATATATTT-T-TAAATAC
1 AATTTTTATAAATTTCTATAAATAC
*
2357535 AATTTTTTTAAATTTCTATAAATA
1 AATTTTTATAAATTTCTATAAATA
2357559 TTTTGAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 13 0.65
24 1 0.05
25 6 0.30
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (25 bp):
AATTTTTATAAATTTCTATAAATAC
Found at i:2357580 original size:20 final size:20
Alignment explanation
Indices: 2357535--2357589 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 20
2357525 TTTTAAATAC
* * * *
2357535 AATTTTTTTAAATTTCTATA
1 AATTATTTTGAATTTTTAAA
2357555 AA-TATTTTGAATTTTTAAA
1 AATTATTTTGAATTTTTAAA
2357574 AATTATTTTG-ATTTTT
1 AATTATTTTGAATTTTT
2357590 TTATAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 21 0.70
20 9 0.30
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (20 bp):
AATTATTTTGAATTTTTAAA
Found at i:2357597 original size:20 final size:20
Alignment explanation
Indices: 2357551--2357597 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
2357541 TTTAAATTTC
*
2357551 TATAAATATTTTGAATTTTT
1 TATAATTATTTTGAATTTTT
* * *
2357571 AAAAATTATTTTGATTTTTT
1 TATAATTATTTTGAATTTTT
2357591 TATAATT
1 TATAATT
2357598 TTTGTTTAGA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (20 bp):
TATAATTATTTTGAATTTTT
Found at i:2367736 original size:24 final size:23
Alignment explanation
Indices: 2367701--2367749 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
2367691 CTGTTTAACA
2367701 TTTACAAATATTTATACGAGTATTT
1 TTTACAAATATTT-TACGA-TATTT
*
2367726 TTTA-AAATATTTTACTATATTT
1 TTTACAAATATTTTACGATATTT
2367748 TT
1 TT
2367750 ATAAGACATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 7 0.30
23 4 0.17
24 8 0.35
25 4 0.17
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (23 bp):
TTTACAAATATTTTACGATATTT
Found at i:2394941 original size:13 final size:13
Alignment explanation
Indices: 2394923--2394948 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2394913 TTCGAAGAAG
2394923 AGGACGATCACCA
1 AGGACGATCACCA
2394936 AGGACGATCACCA
1 AGGACGATCACCA
2394949 GACTTTTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.31, G:0.23, T:0.08
Consensus pattern (13 bp):
AGGACGATCACCA
Found at i:2399065 original size:24 final size:26
Alignment explanation
Indices: 2399017--2399076 Score: 97
Period size: 24 Copynumber: 2.4 Consensus size: 26
2399007 ATAAAAAATA
2399017 ATCAAAATATTATAATTTTTTTATTT
1 ATCAAAATATTATAATTTTTTTATTT
2399043 ATCAAAATATTAT-A-TTTTTTATTT
1 ATCAAAATATTATAATTTTTTTATTT
*
2399067 ACCAAAATAT
1 ATCAAAATAT
2399077 ACCAAAACAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
24 19 0.58
25 1 0.03
26 13 0.39
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.52
Consensus pattern (26 bp):
ATCAAAATATTATAATTTTTTTATTT
Done.