Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 8 of 182
Found at i:2349183 original size:27 final size:27
Alignment explanation
Indices: 2349150--2349299 Score: 162
Period size: 27 Copynumber: 5.6 Consensus size: 27
2349140 TGTAGGATAG
2349150 AATTACCAAAATACCACTAGTTTGTAA
1 AATTACCAAAATACCACTAGTTTGTAA
* *
2349177 AACTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCACTAGTTTGTAA
* * * *
2349204 AATTACCGAAATACCATTGGTTTGTGA
1 AATTACCAAAATACCACTAGTTTGTAA
* *
2349231 AATTACCGAAATACC-CTCAATTTGTAA
1 AATTACCAAAATACCACT-AGTTTGTAA
* *
2349258 AATTACCAAAATACCCCTTA-TTTATAA
1 AATTACCAAAATACCAC-TAGTTTGTAA
2349285 AATTA-CAGAAATACC
1 AATTACCA-AAATACC
2349300 CTTGACTTTC
Statistics
Matches: 105, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
26 3 0.03
27 99 0.94
28 2 0.02
29 1 0.01
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (27 bp):
AATTACCAAAATACCACTAGTTTGTAA
Found at i:2349235 original size:81 final size:81
Alignment explanation
Indices: 2349150--2349299 Score: 223
Period size: 81 Copynumber: 1.9 Consensus size: 81
2349140 TGTAGGATAG
* * *
2349150 AATTACCAAAATACCACT-AGTTTGTAAAACTACCAAAATACCCC-TAGTTTGTAAAATTACCGA
1 AATTACCAAAATACC-CTCAATTTGTAAAACTACCAAAATACCCCTTA-TTTATAAAATTACAGA
2349213 AATACCATTGGTTTGTGA
64 AATACCATTGGTTTGTGA
* *
2349231 AATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTTATTTATAAAATTACAGAAA
1 AATTACCAAAATACCCTCAATTTGTAAAACTACCAAAATACCCCTTATTTATAAAATTACAGAAA
2349296 TACC
66 TACC
2349300 CTTGACTTTC
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
80 2 0.03
81 58 0.94
82 2 0.03
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (81 bp):
AATTACCAAAATACCCTCAATTTGTAAAACTACCAAAATACCCCTTATTTATAAAATTACAGAAA
TACCATTGGTTTGTGA
Found at i:2349360 original size:27 final size:27
Alignment explanation
Indices: 2349150--2349360 Score: 147
Period size: 27 Copynumber: 7.7 Consensus size: 27
2349140 TGTAGGATAG
* * *
2349150 AATTACCAAAATACCAC-TAGTTTGTAA
1 AATTACCGAAATACC-CTTGGTTTATAA
* * * * *
2349177 AACTACCAAAATACCCCTAGTTTGTAA
1 AATTACCGAAATACCCTTGGTTTATAA
* * *
2349204 AATTACCGAAATACCATTGGTTTGTGA
1 AATTACCGAAATACCCTTGGTTTATAA
*** *
2349231 AATTACCGAAATACCCTCAATTTGTAA
1 AATTACCGAAATACCCTTGGTTTATAA
* *
2349258 AATTACCAAAATACCCCTT-ATTTATAA
1 AATTACCGAAATA-CCCTTGGTTTATAA
* * *
2349285 AATTACAGAAATACCCTTGACTTTCTAAA
1 AATTACCGAAATACCCTTG-GTTTAT-AA
** * *
2349314 AATTATAGAAATACCATTGGTTTACAA
1 AATTACCGAAATACCCTTGGTTTATAA
*
2349341 AATTACTGAAATACCCTTGG
1 AATTACCGAAATACCCTTGG
2349361 CTTGTAGATT
Statistics
Matches: 152, Mismatches: 27, Indels: 10
0.80 0.14 0.05
Matches are distributed among these distances:
26 6 0.04
27 116 0.76
28 11 0.07
29 19 0.12
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (27 bp):
AATTACCGAAATACCCTTGGTTTATAA
Found at i:2350330 original size:25 final size:25
Alignment explanation
Indices: 2350292--2350361 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
2350282 AGGAAGTGCT
* *
2350292 AAAAGGGCTCTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCA
*
2350317 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
2350342 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
2350362 ATTAAAAGAG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:2350374 original size:24 final size:24
Alignment explanation
Indices: 2350291--2350374 Score: 98
Period size: 25 Copynumber: 3.4 Consensus size: 24
2350281 GAGGAAGTGC
* *
2350291 TAAAAGGGCTCTGCCCCAGTTTACC
1 TAAAAGGGCTTTGCCCCAGTTTA-T
*
2350316 GAAAAGGGCTTTGCCCCAGTTTAT
1 TAAAAGGGCTTTGCCCCAGTTTAT
*
2350340 CAAAAAGGGCTTTGCCCCAG-TTAT
1 -TAAAAGGGCTTTGCCCCAGTTTAT
2350364 TAAAAGAGGCT
1 TAAAAG-GGCT
2350375 AGGCCTCCAG
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.10
24 8 0.15
25 39 0.75
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.25
Consensus pattern (24 bp):
TAAAAGGGCTTTGCCCCAGTTTAT
Found at i:2350385 original size:50 final size:50
Alignment explanation
Indices: 2350292--2350386 Score: 113
Period size: 50 Copynumber: 1.9 Consensus size: 50
2350282 AGGAAGTGCT
**
2350292 AAAAGGGCTCTGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTCTGCCCCAGTTTACCGAAAAGGGCTAGGCCCCAGTTTATCA
* **
2350342 AAAAGGGCTTTGCCCCAG-TTA-TTAAAAGAGGCTAGGCCTCCAGTT
1 AAAAGGGCTCTGCCCCAGTTTACCGAAAAG-GGCTAGGCC-CCAGTT
2350387 ATATGATAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
48 5 0.13
49 10 0.26
50 23 0.61
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.24
Consensus pattern (50 bp):
AAAAGGGCTCTGCCCCAGTTTACCGAAAAGGGCTAGGCCCCAGTTTATCA
Found at i:2368899 original size:19 final size:20
Alignment explanation
Indices: 2368864--2368903 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
2368854 TGCATTCCAT
*
2368864 AACTCAAGATAACATAAAAA
1 AACTCAAGATAAAATAAAAA
2368884 AACTCAA-ATAAAATAAAAA
1 AACTCAAGATAAAATAAAAA
2368903 A
1 A
2368904 TAATGTTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.70, C:0.12, G:0.03, T:0.15
Consensus pattern (20 bp):
AACTCAAGATAAAATAAAAA
Found at i:2378265 original size:29 final size:29
Alignment explanation
Indices: 2378233--2378309 Score: 111
Period size: 29 Copynumber: 2.7 Consensus size: 29
2378223 ATTCATATTC
2378233 ATATGGCCCATTAGGCCCAAATCATC-TGT
1 ATATGGCCCATTAGGCCCAAATCA-CATGT
*
2378262 ATATGGCCCATTAGGCCCAAATCACATTT
1 ATATGGCCCATTAGGCCCAAATCACATGT
* *
2378291 ATATGGCCCGTTTGGCCCA
1 ATATGGCCCATTAGGCCCA
2378310 GTCAAATTCA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
28 1 0.02
29 43 0.98
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (29 bp):
ATATGGCCCATTAGGCCCAAATCACATGT
Found at i:2379844 original size:16 final size:17
Alignment explanation
Indices: 2379813--2379851 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
2379803 ACAAAGAGAG
2379813 TTTGGGATTTCAGGATT
1 TTTGGGATTTCAGGATT
*
2379830 TTTGGG-TTTCGGGATT
1 TTTGGGATTTCAGGATT
2379846 TTTGGG
1 TTTGGG
2379852 GCATTACAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.10, C:0.05, G:0.36, T:0.49
Consensus pattern (17 bp):
TTTGGGATTTCAGGATT
Found at i:2382079 original size:16 final size:17
Alignment explanation
Indices: 2382058--2382090 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2382048 GGGAATGTGT
2382058 GTGGTGAAGG-TTTGCA
1 GTGGTGAAGGATTTGCA
*
2382074 GTGGTGATGGATTTGCA
1 GTGGTGAAGGATTTGCA
2382091 ACAGCAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.18, C:0.06, G:0.42, T:0.33
Consensus pattern (17 bp):
GTGGTGAAGGATTTGCA
Found at i:2389470 original size:48 final size:48
Alignment explanation
Indices: 2389350--2389472 Score: 201
Period size: 48 Copynumber: 2.6 Consensus size: 48
2389340 TGATATGTGT
* *
2389350 GCTAGTGTAAGACATGTCTAGAACATGCATCGGCCTTGAGATATACAA
1 GCTAGTGTAAGACATGTCTAGGACATGCATCGGCCTTGAGACATACAA
*
2389398 GCCAGTGTAAGACATGTCTAGGACATGCATCGGCCTTGAGACATACAA
1 GCTAGTGTAAGACATGTCTAGGACATGCATCGGCCTTGAGACATACAA
* *
2389446 GCTAGTGTAAGACCTGTCTGGGACATG
1 GCTAGTGTAAGACATGTCTAGGACATG
2389473 GCGTCAGCTT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 69 1.00
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (48 bp):
GCTAGTGTAAGACATGTCTAGGACATGCATCGGCCTTGAGACATACAA
Found at i:2389571 original size:49 final size:49
Alignment explanation
Indices: 2389400--2389622 Score: 151
Period size: 49 Copynumber: 4.7 Consensus size: 49
2389390 ATATACAAGC
* * * * * *
2389400 CAGTGTAAGACATGTCTAGGACAT-GCATCGGCCTTGAGACAT-ACAAG-
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATGA-AAGT
* * * * *
2389447 CTAGTGTAAGACCTGTCTGGGACATGGCGTC-AGCTTG-TTG-TG--TGT
1 C-AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATGAAAGT
* * * *
2389492 CAGTGTAAAACCTTTCCGGGACATGGCATCGACACT-GATAGATGAGAG-
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGAC-CTCGATAGATGAAAGT
* * * * *
2389540 CTAGTGTAAGACCTGTCTGGGACACGACATCGGCCTCTATATATGAAAGT
1 C-AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATGAAAGT
*
2389590 CAGTGTAAGACCTGTCTGGAACATGGCATCGAC
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGAC
2389623 TTTGATATGC
Statistics
Matches: 134, Mismatches: 29, Indels: 24
0.72 0.16 0.13
Matches are distributed among these distances:
44 26 0.19
45 3 0.02
46 5 0.04
47 3 0.02
48 28 0.21
49 68 0.51
50 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (49 bp):
CAGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATGAAAGT
Found at i:2393606 original size:48 final size:48
Alignment explanation
Indices: 2393493--2393644 Score: 177
Period size: 48 Copynumber: 3.2 Consensus size: 48
2393483 TATGTGTGCT
* * * *
2393493 AGTGTAAGACATGTTTGGGACATGCATTGACC-ACA-TTAT-CAGAGCC
1 AGTGTAAGACATGTTTGGGACATGCATCGGCCTCCAGATATACA-AGCC
*
2393539 AGTGTAAGACATGTTTGGGATATGCATCGGCCTCCAGATATACAAGCC
1 AGTGTAAGACATGTTTGGGACATGCATCGGCCTCCAGATATACAAGCC
* * * *
2393587 AGTGTAAGACATGTCTGGGACATGCATTC-GCCTCGAGATATACAGGCT
1 AGTGTAAGACATGTTTGGGACATGCA-TCGGCCTCCAGATATACAAGCC
2393635 AGTGTAAGAC
1 AGTGTAAGAC
2393645 CTATCTGAGA
Statistics
Matches: 92, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
46 29 0.32
47 2 0.02
48 57 0.62
49 4 0.04
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.25
Consensus pattern (48 bp):
AGTGTAAGACATGTTTGGGACATGCATCGGCCTCCAGATATACAAGCC
Found at i:2393657 original size:48 final size:48
Alignment explanation
Indices: 2393535--2393658 Score: 142
Period size: 48 Copynumber: 2.6 Consensus size: 48
2393525 ACATTATCAG
* * * *
2393535 AGCCAGTGTAAGACATGTTTGGGATATGCATCGGCCTCCAGATATACA
1 AGCCAGTGTAAGACATATCTGAGACATGCATCGGCCTCCAGATATACA
* * *
2393583 AGCCAGTGTAAGACATGTCTGGGACATGCATTC-GCCTCGAGATATACA
1 AGCCAGTGTAAGACATATCTGAGACATGCA-TCGGCCTCCAGATATACA
* * *
2393631 GGCTAGTGTAAGACCTATCTGAGACATG
1 AGCCAGTGTAAGACATATCTGAGACATG
2393659 GCGTCAGCTT
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
48 65 0.97
49 2 0.03
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (48 bp):
AGCCAGTGTAAGACATATCTGAGACATGCATCGGCCTCCAGATATACA
Found at i:2393701 original size:44 final size:47
Alignment explanation
Indices: 2393632--2393749 Score: 134
Period size: 44 Copynumber: 2.6 Consensus size: 47
2393622 AGATATACAG
* * * * * *
2393632 GCTAGTGTAAGACCTATCTGAGACATGGCGTCAGC-TTGTTGTG-T-
1 GCTAGTGTAAGACCTGTCTGGGACATGGCATCAACTTTGATATGCTA
*
2393676 GTTAGTGTAAGACCTGTCTGGGACATGGCATCAACTTTGATATGCTA
1 GCTAGTGTAAGACCTGTCTGGGACATGGCATCAACTTTGATATGCTA
*
2393723 GCCAGTGTAAGACCGTGTCTGGGACAT
1 GCTAGTGTAAGACC-TGTCTGGGACAT
2393750 TGGGTCGGTA
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
44 30 0.49
45 6 0.10
46 1 0.02
47 12 0.20
48 12 0.20
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.30
Consensus pattern (47 bp):
GCTAGTGTAAGACCTGTCTGGGACATGGCATCAACTTTGATATGCTA
Found at i:2398997 original size:39 final size:39
Alignment explanation
Indices: 2398936--2399081 Score: 177
Period size: 39 Copynumber: 3.7 Consensus size: 39
2398926 CACGACACGA
* * * *
2398936 AAGTGCTATCAAGAGTACCGAAGTACAACTGGGGCATGT
1 AAGTGCGATCAGGGGTACCGAAGTACGACTGGGGCATGT
*
2398975 AAGTGCGATCAGGGGTATCGAAGTACGA-TAGGGGCATGT
1 AAGTGCGATCAGGGGTACCGAAGTACGACT-GGGGCATGT
* * * * * *
2399014 AAGTGCGATTAGGGGTACTGATGTACGACAGGGACACGT
1 AAGTGCGATCAGGGGTACCGAAGTACGACTGGGGCATGT
2399053 AAGTGCGATCAGGGGTACCGAAGTACGAC
1 AAGTGCGATCAGGGGTACCGAAGTACGAC
2399082 AAGGGCACAT
Statistics
Matches: 90, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 89 0.99
ACGTcount: A:0.30, C:0.16, G:0.34, T:0.19
Consensus pattern (39 bp):
AAGTGCGATCAGGGGTACCGAAGTACGACTGGGGCATGT
Found at i:2398998 original size:20 final size:19
Alignment explanation
Indices: 2398975--2399076 Score: 73
Period size: 20 Copynumber: 5.2 Consensus size: 19
2398965 TGGGGCATGT
2398975 AAGTGCGATCAGGGGTATCG
1 AAGTGCGATCAGGGGTA-CG
* * *
2398995 AAGTACGAT-AGGGGCATG
1 AAGTGCGATCAGGGGTACG
*
2399013 TAAGTGCGATTAGGGGTACTG
1 -AAGTGCGATCAGGGGTAC-G
* * **
2399034 ATGTACGA-CAGGGACACG
1 AAGTGCGATCAGGGGTACG
2399052 TAAGTGCGATCAGGGGTACCG
1 -AAGTGCGATCAGGGGTA-CG
2399073 AAGT
1 AAGT
2399077 ACGACAAGGG
Statistics
Matches: 61, Mismatches: 15, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
18 2 0.03
19 26 0.43
20 30 0.49
21 3 0.05
ACGTcount: A:0.28, C:0.15, G:0.37, T:0.20
Consensus pattern (19 bp):
AAGTGCGATCAGGGGTACG
Found at i:2399017 original size:19 final size:19
Alignment explanation
Indices: 2398966--2399028 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 19
2398956 AAGTACAACT
2398966 GGGGCATGTAAGTGCGATCA
1 GGGGCATGTAAGTGCGAT-A
* *
2398986 GGGGTATCG-AAGTACGATA
1 GGGGCAT-GTAAGTGCGATA
2399005 GGGGCATGTAAGTGCGATTA
1 GGGGCATGTAAGTGCGA-TA
2399025 GGGG
1 GGGG
2399029 TACTGATGTA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 1 0.03
19 14 0.39
20 20 0.56
21 1 0.03
ACGTcount: A:0.25, C:0.11, G:0.43, T:0.21
Consensus pattern (19 bp):
GGGGCATGTAAGTGCGATA
Found at i:2399082 original size:39 final size:39
Alignment explanation
Indices: 2398929--2399095 Score: 174
Period size: 39 Copynumber: 4.3 Consensus size: 39
2398919 ATGTAACCAC
* * * * * *
2398929 GACACGAAAGTGCTATCAAGAGTACCGAAGTACAACTGG
1 GACACGTAAGTGCGATCAGGGGTACCGAAGTACGACAGG
* * * *
2398968 GGCATGTAAGTGCGATCAGGGGTATCGAAGTACGATAGG
1 GACACGTAAGTGCGATCAGGGGTACCGAAGTACGACAGG
* * * * *
2399007 GGCATGTAAGTGCGATTAGGGGTACTGATGTACGACAGG
1 GACACGTAAGTGCGATCAGGGGTACCGAAGTACGACAGG
2399046 GACACGTAAGTGCGATCAGGGGTACCGAAGTACGACAAGG
1 GACACGTAAGTGCGATCAGGGGTACCGAAGTACGAC-AGG
*
2399086 G-CACATAAGT
1 GACACGTAAGT
2399096 ACAACCCGGG
Statistics
Matches: 106, Mismatches: 21, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
39 102 0.96
40 4 0.04
ACGTcount: A:0.32, C:0.17, G:0.34, T:0.18
Consensus pattern (39 bp):
GACACGTAAGTGCGATCAGGGGTACCGAAGTACGACAGG
Found at i:2404998 original size:54 final size:53
Alignment explanation
Indices: 2404871--2405202 Score: 372
Period size: 54 Copynumber: 6.5 Consensus size: 53
2404861 TGAGGTCACA
* * * * * * *
2404871 TGTGTAGTATTAAGTGCAGGCTACTATGCGTACCTGAAAACT-GTGA--TCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACGTCA-G
*
2404922 TGAGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACGTCATG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACGTCA-G
2404976 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACGTCATG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACGTCA-G
* * * *
2405030 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATC--A-GA-TGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACGTCA-G
2405080 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCA---C-G
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACGTCAG
* * *
2405129 TGTGTAGTACTAAGTACAGGCTACTA-TTGTACCGGATAATT-G-CTCG-CA-
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACGTCAG
*
2405177 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
2405203 TGCATACCAA
Statistics
Matches: 248, Mismatches: 23, Indels: 23
0.84 0.08 0.08
Matches are distributed among these distances:
46 1 0.00
47 1 0.00
48 39 0.16
49 26 0.10
50 43 0.17
51 37 0.15
52 5 0.02
53 1 0.00
54 95 0.38
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (53 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACGTCAG
Found at i:2405109 original size:104 final size:101
Alignment explanation
Indices: 2404863--2405202 Score: 368
Period size: 104 Copynumber: 3.3 Consensus size: 101
2404853 ATCTATTGTG
* * * * * * * *
2404863 AGGTCACATGTGTAGTATTAAGTGCAGGCTACTATGCGTACCTGAAAACT-GTGATCACGTGAGT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCATCA-GTGTGT
* **
2404927 AGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
65 AGTACTAAGTGCAGGCTACTACGTGTACCAGATGGTT
2404964 -GGTCACGTCATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACGTCA
1 AGGTCA---CA--TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCA--TCA
*
2405028 TGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
59 -GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGTT
*
2405072 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCA-C-GTGTGTA
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCATCAGTGTGTA
* * * **
2405135 GTACTAAGTACAGGCTACTA-TTGTACCGGATAATT
66 GTACTAAGTGCAGGCTACTACGTGTACCAGATGGTT
* * *
2405170 -GCTCGCATGTGTAGTACTATGTGCAGGCTACTA
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTA
2405203 TGCATACCAA
Statistics
Matches: 206, Mismatches: 24, Indels: 22
0.82 0.10 0.09
Matches are distributed among these distances:
97 29 0.14
98 10 0.05
99 26 0.13
100 5 0.02
101 1 0.00
103 2 0.01
104 47 0.23
105 36 0.17
106 4 0.02
108 41 0.20
109 5 0.02
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (101 bp):
AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCATCAGTGTGTA
GTACTAAGTGCAGGCTACTACGTGTACCAGATGGTT
Found at i:2407841 original size:35 final size:34
Alignment explanation
Indices: 2407800--2407882 Score: 103
Period size: 35 Copynumber: 2.4 Consensus size: 34
2407790 CTGATATGAT
**
2407800 AATGGGCTAAGGCCCAGACTGCTACTGTTACTGA
1 AATGGGCTAAGGCCCAGACTGCTACTACTACTGA
** *
2407834 AATTGGGCTCTGGCCTAGACTGCTACTACTACTGA
1 AA-TGGGCTAAGGCCCAGACTGCTACTACTACTGA
*
2407869 AATAGGCTAAGGCC
1 AATGGGCTAAGGCC
2407883 TAACTGAACC
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
34 11 0.28
35 29 0.73
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (34 bp):
AATGGGCTAAGGCCCAGACTGCTACTACTACTGA
Found at i:2420700 original size:55 final size:55
Alignment explanation
Indices: 2420567--2420701 Score: 135
Period size: 55 Copynumber: 2.5 Consensus size: 55
2420557 GACATGGCCG
* ** * * ** **
2420567 TGGGCGAACCTGCCAAAACAACACGGGTGTGTGACACGCTCGTGCCTTGAAACTG
1 TGGGCGAACCTGCCAAAACAACACGAGCCTGCGACACGCCCGTGCCAAGAAACCA
* * ** *
2420622 TGGCCGAACCTGTCAAATTAACACGAGCCTGCGACACGCCCGTGCCAAGCAACCA
1 TGGGCGAACCTGCCAAAACAACACGAGCCTGCGACACGCCCGTGCCAAGAAACCA
*
2420677 TGGGTGAACCTGCCAAAACAACACG
1 TGGGCGAACCTGCCAAAACAACACG
2420702 GGCGCGGCCC
Statistics
Matches: 61, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
55 61 1.00
ACGTcount: A:0.29, C:0.31, G:0.25, T:0.15
Consensus pattern (55 bp):
TGGGCGAACCTGCCAAAACAACACGAGCCTGCGACACGCCCGTGCCAAGAAACCA
Found at i:2440857 original size:48 final size:45
Alignment explanation
Indices: 2440782--2440904 Score: 142
Period size: 48 Copynumber: 2.6 Consensus size: 45
2440772 TGTGTACTAA
*
2440782 TGTAAGACATATCTAGGACATGCATCGGCCACATT-ATGAGAGCCAG
1 TGTAAGACATGTCTAGGACATGCATCGG-C-CATTGATGAGAGCCAG
* * *
2440828 TGTAAGACCATGTTTGGGACATTGCATCGG-CATTGAGATGAGAGCTAG
1 TGTAAGA-CATGTCTAGGACA-TGCATCGGCCATT--GATGAGAGCCAG
2440876 TGTAAGACATGTCTAGGACATGCATCGGC
1 TGTAAGACATGTCTAGGACATGCATCGGC
2440905 TTTGAGATGT
Statistics
Matches: 65, Mismatches: 6, Indels: 11
0.79 0.07 0.13
Matches are distributed among these distances:
45 4 0.06
46 15 0.23
47 21 0.32
48 25 0.38
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (45 bp):
TGTAAGACATGTCTAGGACATGCATCGGCCATTGATGAGAGCCAG
Found at i:2440924 original size:46 final size:45
Alignment explanation
Indices: 2440782--2440935 Score: 148
Period size: 46 Copynumber: 3.3 Consensus size: 45
2440772 TGTGTACTAA
* *** * *
2440782 TGTAAGACATATCTAGGACATGCATCGGCCACATTATGAGAGCCAG
1 TGTAAGACATGTCTAGGACATGCATCGGCTTGA-GATGAGAGCAAG
* * *
2440828 TGTAAGACCATGTTTGGGACATTGCATCGGCATTGAGATGAGAGCTAG
1 TGTAAGA-CATGTCTAGGACA-TGCATCGGC-TTGAGATGAGAGCAAG
2440876 TGTAAGACATGTCTAGGACATGCATCGGCTTTGAGATGTA-AGCAAG
1 TGTAAGACATGTCTAGGACATGCATCGGC-TTGAGATG-AGAGCAAG
* *
2440922 TGTAGGACGTGTCT
1 TGTAAGACATGTCT
2440936 TGGATAGCCA
Statistics
Matches: 90, Mismatches: 14, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
46 41 0.46
47 22 0.24
48 26 0.29
49 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.26
Consensus pattern (45 bp):
TGTAAGACATGTCTAGGACATGCATCGGCTTGAGATGAGAGCAAG
Found at i:2460617 original size:48 final size:48
Alignment explanation
Indices: 2460565--2460689 Score: 150
Period size: 46 Copynumber: 2.6 Consensus size: 48
2460555 CCACATTATG
2460565 AGAGCCAGTGTAAGACCATGTCTGGGACATAGCATCGGCATTGA-A-ACA
1 AGAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATTGAGATACA
* * * **
2460613 AGAGCTAGTGTATGACATGTCTGGGACATGCATCGGCCTTGAGATGTA
1 AGAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGATACA
*
2460661 A-A-CCAGTGTAAGACGTGTCTGGGACATGC
1 AGAGCCAGTGTAAGACATGTCTGGGACATGC
2460690 TTTGGCTATG
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
46 36 0.54
47 16 0.24
48 15 0.22
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.22
Consensus pattern (48 bp):
AGAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGATACA
Found at i:2462341 original size:7 final size:7
Alignment explanation
Indices: 2462329--2462358 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
2462319 TGAAGAATGT
2462329 GTCTGAA
1 GTCTGAA
2462336 GTCTGAA
1 GTCTGAA
2462343 GTCTGAA
1 GTCTGAA
2462350 GTCTGAA
1 GTCTGAA
2462357 GT
1 GT
2462359 TTTCTAGGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.27, C:0.13, G:0.30, T:0.30
Consensus pattern (7 bp):
GTCTGAA
Found at i:2468424 original size:46 final size:46
Alignment explanation
Indices: 2468336--2468554 Score: 187
Period size: 46 Copynumber: 4.7 Consensus size: 46
2468326 TTATTTGTGT
* * *
2468336 GCCAGTATAAGA-TATGTCTGGGACATGCATCGGCCTCGAGATGTAA
1 GCCAGTGTAAGACCATGTCTGGGACATGCATCGGCCTCAAGATGT-A
2468382 GCCAGTGTAAGA-CATGTCTGGGACATGCATCGG-CTACAAGATGT-
1 GCCAGTGTAAGACCATGTCTGGGACATGCATCGGCCT-CAAGATGTA
* * * * **
2468426 GTCAGTCTAAGACCATGTCTAGGACATGGCGTCGGCCTCAATTTTGATA
1 GCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGCCTCAA-GATG-TA
* * * * * *
2468475 GTCAATGTAAGACCATGTCTGGGACATGGCATCGACTTGATGGATG-A
1 GCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGCCTCA-AGATGTA
*
2468522 GCCAGTGTAAGACCATGTTTGGGACATGACATC
1 GCCAGTGTAAGACCATGTCTGGGACATG-CATC
2468555 TGTAACAGCC
Statistics
Matches: 142, Mismatches: 22, Indels: 17
0.78 0.12 0.09
Matches are distributed among these distances:
44 10 0.07
45 15 0.11
46 48 0.34
47 33 0.23
48 1 0.01
49 35 0.25
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (46 bp):
GCCAGTGTAAGACCATGTCTGGGACATGCATCGGCCTCAAGATGTA
Found at i:2486551 original size:24 final size:25
Alignment explanation
Indices: 2486519--2486568 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
2486509 TAATAATAGA
*
2486519 ATATAAATAAAAATAATTAT-TAAT
1 ATATAAATAAAAATAAATATATAAT
*
2486543 ATATAAATAAAGATAAATATATAAT
1 ATATAAATAAAAATAAATATATAAT
2486568 A
1 A
2486569 CAGGTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (25 bp):
ATATAAATAAAAATAAATATATAAT
Found at i:2486636 original size:19 final size:19
Alignment explanation
Indices: 2486614--2486702 Score: 71
Period size: 19 Copynumber: 4.7 Consensus size: 19
2486604 TAAAAATGTA
*
2486614 TAATAATATA-AAAATGACT
1 TAATAATATATAAAAT-AAT
2486633 TAATAATATATAAAATAAT
1 TAATAATATATAAAATAAT
*
2486652 T-ATAATATATAATATAA-
1 TAATAATATATAAAATAAT
*
2486669 -AAGCATATATATAAAAATAA-
1 TAA-TA-ATATAT-AAAATAAT
2486689 TATATAATATATAA
1 TA-ATAATATATAA
2486703 TAAACATATA
Statistics
Matches: 58, Mismatches: 5, Indels: 14
0.75 0.06 0.18
Matches are distributed among these distances:
17 1 0.02
18 16 0.28
19 21 0.36
20 17 0.29
21 2 0.03
22 1 0.02
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (19 bp):
TAATAATATATAAAATAAT
Found at i:2486670 original size:23 final size:24
Alignment explanation
Indices: 2486616--2486726 Score: 81
Period size: 25 Copynumber: 4.7 Consensus size: 24
2486606 AAAATGTATA
*
2486616 ATAATATAAAA-ATGACT-TAATA-
1 ATAATATAAAATAT-ATTATAATAT
2486638 AT-ATATAAAATA-ATTATAATAT
1 ATAATATAAAATATATTATAATAT
* *
2486660 ATAATATAAAAGCATATATATAA-AA
1 ATAATATAAAA-TATAT-TATAATAT
* * *
2486685 ATAATATATAATATATAATAAACAT
1 ATAATATAAAATATATTAT-AATAT
2486710 ATAATATAATAATATAT
1 ATAATATAA-AATATAT
2486727 AAATAATGAT
Statistics
Matches: 71, Mismatches: 8, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
20 2 0.03
21 13 0.18
22 5 0.07
23 10 0.14
24 7 0.10
25 22 0.31
26 12 0.17
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (24 bp):
ATAATATAAAATATATTATAATAT
Found at i:2486706 original size:37 final size:36
Alignment explanation
Indices: 2486638--2486728 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 36
2486628 TGACTTAATA
2486638 ATATATAAAATAAT-TATAATATATAATATAAAAGCAT
1 ATATATAAAATAATATATAATATATAATAT-AAA-CAT
2486675 ATATATAAAAATAATATATAATATAT-A-ATAAACAT
1 ATATAT-AAAATAATATATAATATATAATATAAACAT
*
2486710 ATA-ATATAATAATATATAA
1 ATATATAAAATAATATATAA
2486729 ATAATGATGT
Statistics
Matches: 51, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
33 13 0.25
34 2 0.04
35 6 0.12
36 3 0.06
37 8 0.16
38 9 0.18
39 10 0.20
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (36 bp):
ATATATAAAATAATATATAATATATAATATAAACAT
Found at i:2486711 original size:18 final size:18
Alignment explanation
Indices: 2486635--2486723 Score: 60
Period size: 18 Copynumber: 4.7 Consensus size: 18
2486625 AAATGACTTA
2486635 ATAATATATAA-AATA-ATT
1 ATAATATATAATAA-ACA-T
2486653 ATAATATATAATATAAAAGCAT
1 ATAATATAT-A-AT-AAA-CAT
* *
2486675 AT-ATATA-AAAATAATAT
1 ATAATATATAATA-AACAT
2486692 ATAATATATAATAAACAT
1 ATAATATATAATAAACAT
2486710 ATAATATAATAATA
1 ATAATAT-ATAATA
2486724 TATAAATAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 19
0.71 0.05 0.24
Matches are distributed among these distances:
17 5 0.09
18 28 0.49
19 11 0.19
20 1 0.02
21 6 0.11
22 5 0.09
23 1 0.02
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (18 bp):
ATAATATATAATAAACAT
Found at i:2486729 original size:23 final size:22
Alignment explanation
Indices: 2486673--2486727 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 22
2486663 ATATAAAAGC
2486673 ATATATATAAAAATAATATATA
1 ATATATATAAAAATAATATATA
2486695 ATATATAATAAACATATAATATAATA
1 ATATAT-ATAAA-A-ATAATAT-ATA
2486721 ATATATA
1 ATATATA
2486728 AATAATGATG
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
22 6 0.21
23 5 0.17
24 1 0.03
25 8 0.28
26 9 0.31
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
ATATATATAAAAATAATATATA
Found at i:2486733 original size:37 final size:36
Alignment explanation
Indices: 2486638--2486742 Score: 101
Period size: 35 Copynumber: 2.9 Consensus size: 36
2486628 TGACTTAATA
* *
2486638 ATATATAAAATAAT-TAT-AATATATAATATAAAAGC
1 ATATATATAATAATATATAAATA-ATAATATAAAAAC
* *
2486673 ATATATATAAAAATA-ATATATAAT-ATATAATAAAC
1 ATATATATAATAATATATAAATAATAATATAA-AAAC
* *
2486708 ATATAATATAATAATATATAAATAATGATGTAAAA
1 ATAT-ATATAATAATATATAAATAATAATATAAAA
2486743 TAATAATTCG
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
34 6 0.11
35 23 0.40
36 13 0.23
37 10 0.18
38 5 0.09
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (36 bp):
ATATATATAATAATATATAAATAATAATATAAAAAC
Found at i:2486745 original size:27 final size:26
Alignment explanation
Indices: 2486687--2486749 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
2486677 ATATAAAAAT
2486687 AATATATAATATATAATAAACATATAA
1 AATA-ATAATATATAATAAACATATAA
* ** *
2486714 TATAATAATATATAAATAATGATGTAA
1 AATAATAATATAT-AATAAACATATAA
2486741 AATAATAAT
1 AATAATAAT
2486750 TCGTGAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 9 0.30
27 21 0.70
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (26 bp):
AATAATAATATATAATAAACATATAA
Found at i:2486790 original size:9 final size:10
Alignment explanation
Indices: 2486758--2486806 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
2486748 ATTCGTGAAA
2486758 AATAATATAT
1 AATAATATAT
*
2486768 AAGAA-ATAAT
1 AATAATAT-AT
2486778 AATAATATA-
1 AATAATATAT
2486787 AATAATATAT
1 AATAATATAT
*
2486797 AATAAAATAT
1 AATAATATAT
2486807 TTTTATAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
9 11 0.33
10 20 0.61
11 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (10 bp):
AATAATATAT
Found at i:2488730 original size:210 final size:210
Alignment explanation
Indices: 2488262--2488820 Score: 686
Period size: 210 Copynumber: 2.7 Consensus size: 210
2488252 AAATCTGCTT
* * * * *
2488262 CTTCGATTTGTTCTCTGATAATACAGAGATGCCAAATTATCTTAGATTTACTTCATCGTAAGCAC
1 CTTCGATTTGTTCTCTGAAAATACAGAGATGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
* * * ** * * * **
2488327 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTG--TAA-GCACAA-TGAT---GTCAAA
66 GTGAAAGCCAAATCAGCTATATCTTCGATCTGCTCCCCGCCGAATACA-AAGAGATAAGGTC-TG
* * * * *
2488385 TCATCTTGGATCTTGCATCAGTCTAATCGTCTAAAGGTCAGATCTGCTATGTATCTGCTCTCCAT
129 TCATCTTGGATC-TGCATCAGTCTAAACATCTAAAGGTAAGATCTACTATGTATCTCCTCTCCAT
** *
2488450 TGAAGTAGAGATGCCAGA
193 CAAAGTAGAAATGCCAGA
*
2488468 CTTCGATTTGTTCTCTGAAAATATAGAGATGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
1 CTTCGATTTGTTCTCTGAAAATACAGAGATGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
2488533 GTGAAAGCCAAATCAGCTATATCTTCGATCTGCTCCCCGCCGAATACAAAGAGATAAGGTCTGTC
66 GTGAAAGCCAAATCAGCTATATCTTCGATCTGCTCCCCGCCGAATACAAAGAGATAAGGTCTGTC
* * *
2488598 ATCTTGGATCTGCTTCAG-CGTAAACATCTGAAGGTAAGATCTACTATGTGTCTACCT-TCCATC
131 ATCTTGGATCTGCATCAGTC-TAAACATCTAAAGGTAAGATCTACTATGTATCT-CCTCTCCATC
* *
2488661 AAAGTGGAAATGGCAGA
194 AAAGTAGAAATGCCAGA
* * * *
2488678 CTTCGATTTGTTCTCTGACAATACAGAGACGATAAATCATCTTAGATTTGCTTCATCATAAACAC
1 CTTCGATTTGTTCTCTGAAAATACAGAGATGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
* * *
2488743 GTGAAAGCCAAATCAGCTATATCTTCGATCTACTCCCCGCCGAATACAGAGAGATAAGATCTGTC
66 GTGAAAGCCAAATCAGCTATATCTTCGATCTGCTCCCCGCCGAATACAAAGAGATAAGGTCTGTC
2488808 ATCTTGGATCTGC
131 ATCTTGGATCTGC
2488821 CTTGATGAAG
Statistics
Matches: 307, Mismatches: 37, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
206 93 0.30
208 4 0.01
209 6 0.02
210 187 0.61
211 14 0.05
212 3 0.01
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.31
Consensus pattern (210 bp):
CTTCGATTTGTTCTCTGAAAATACAGAGATGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
GTGAAAGCCAAATCAGCTATATCTTCGATCTGCTCCCCGCCGAATACAAAGAGATAAGGTCTGTC
ATCTTGGATCTGCATCAGTCTAAACATCTAAAGGTAAGATCTACTATGTATCTCCTCTCCATCAA
AGTAGAAATGCCAGA
Found at i:2506574 original size:3 final size:3
Alignment explanation
Indices: 2506561--2506783 Score: 72
Period size: 3 Copynumber: 71.3 Consensus size: 3
2506551 TTAAAACCTT
* * * * *
2506561 TAA TGA TAA TAA TATA TAGA TAA AAA TGTA TAA TAA T-A TAA AAA TGACT
1 TAA TAA TAA TAA TA-A TA-A TAA TAA T-AA TAA TAA TAA TAA TAA T-A-A
* *
2506610 TAA TAA TATA TAA -AA TAA TTA TAA TATA TAA T-A TAA -AA GCAA TATA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA -TAA TA-A
*
2506656 TAA AAA TAA TATA TAA TATA TAA TAA -ACA T-A TAA T-A TAA TAA TATA
1 TAA TAA TAA TA-A TAA TA-A TAA TAA TA-A TAA TAA TAA TAA TAA TA-A
* * ** *
2506702 TAAA TAA TGA T-G TAA -AA TAA TAA TTTG TGAA AAA TAA TATA TAA TAAA
1 T-AA TAA TAA TAA TAA TAA TAA TAA -TAA T-AA TAA TAA TA-A TAA T-AA
2506750 TAA TAA TAA T-A TAAA TAA TATA TAA TAA -AA TAA T
1 TAA TAA TAA TAA T-AA TAA TA-A TAA TAA TAA TAA T
2506784 TTTATAATAT
Statistics
Matches: 165, Mismatches: 25, Indels: 60
0.66 0.10 0.24
Matches are distributed among these distances:
2 20 0.12
3 100 0.61
4 43 0.26
5 2 0.01
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2506639 original size:7 final size:7
Alignment explanation
Indices: 2506612--2506801 Score: 102
Period size: 7 Copynumber: 28.1 Consensus size: 7
2506602 AAATGACTTA
2506612 ATAATAT
1 ATAATAT
2506619 ATAA-A-
1 ATAATAT
2506624 ATAAT-T
1 ATAATAT
2506630 ATAATAT
1 ATAATAT
2506637 ATAATAT
1 ATAATAT
2506644 A-AA-A-
1 ATAATAT
**
2506648 GCAATAT
1 ATAATAT
*
2506655 ATAA-AA
1 ATAATAT
2506661 ATAATAT
1 ATAATAT
2506668 ATAATAT
1 ATAATAT
2506675 AT-A-AT
1 ATAATAT
*
2506680 A-AACAT
1 ATAATAT
2506686 ATAATAT
1 ATAATAT
2506693 AATAATAT
1 -ATAATAT
2506701 ATAA-AT
1 ATAATAT
* *
2506707 AATGATGT
1 -ATAATAT
*
2506715 AAAATA-
1 ATAATAT
*
2506721 ATAATTT
1 ATAATAT
* *
2506728 GTGAA-AA
1 AT-AATAT
2506735 ATAATAT
1 ATAATAT
*
2506742 ATAATAA
1 ATAATAT
2506749 ATAATA-
1 ATAATAT
2506755 ATAATAT
1 ATAATAT
2506762 AAATAATAT
1 --ATAATAT
*
2506771 ATAATAAA
1 ATAAT-AT
*
2506779 ATAATTTT
1 ATAA-TAT
2506787 ATAATAT
1 ATAATAT
2506794 ATAATAT
1 ATAATAT
2506801 A
1 A
2506802 AAAATAAGGT
Statistics
Matches: 139, Mismatches: 23, Indels: 42
0.68 0.11 0.21
Matches are distributed among these distances:
5 11 0.08
6 32 0.23
7 69 0.50
8 19 0.14
9 8 0.06
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.36
Consensus pattern (7 bp):
ATAATAT
Found at i:2506640 original size:13 final size:13
Alignment explanation
Indices: 2506612--2506807 Score: 76
Period size: 13 Copynumber: 15.1 Consensus size: 13
2506602 AAATGACTTA
2506612 ATAATATATAAA-
1 ATAATATATAAAT
2506624 ATAAT-TATAATAT
1 ATAATATATAA-AT
2506637 ATAATATA-AAA-
1 ATAATATATAAAT
** *
2506648 GCAATATATAAAA
1 ATAATATATAAAT
2506661 ATAATATAT-AAT
1 ATAATATATAAAT
*
2506673 AT-ATA-ATAAAC
1 ATAATATATAAAT
*
2506684 AT-ATA-ATATA-
1 ATAATATATAAAT
2506694 ATAATATATAAAT
1 ATAATATATAAAT
* *
2506707 AATGATGTA-AAAT
1 -ATAATATATAAAT
* * *
2506720 AATAATTTGTGAAAA
1 -ATAATATAT-AAAT
2506735 ATAATATATAATAAAT
1 AT-A-ATAT-ATAAAT
2506751 AATAATAATATAAAT
1 -ATAAT-ATATAAAT
2506766 A-ATATATAATAAA-
1 ATA-ATAT-ATAAAT
*
2506779 ATAATTTTATAATAT
1 ATAA-TATATAA-AT
*
2506794 ATAATATAAAAAT
1 ATAATATATAAAT
2506807 A
1 A
2506808 AGGTTAAAAA
Statistics
Matches: 141, Mismatches: 20, Indels: 45
0.68 0.10 0.22
Matches are distributed among these distances:
10 4 0.03
11 28 0.20
12 18 0.13
13 36 0.26
14 27 0.19
15 16 0.11
16 9 0.06
17 3 0.02
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (13 bp):
ATAATATATAAAT
Found at i:2506668 original size:31 final size:33
Alignment explanation
Indices: 2506630--2506708 Score: 101
Period size: 31 Copynumber: 2.5 Consensus size: 33
2506620 TAAAATAATT
* *
2506630 ATAATATATAATATAAAAGCAATATATAA-A-A
1 ATAATATATAATATAAAAGAAACATATAATATA
* *
2506661 ATAATATATAATATATAATAAACATATAATATA
1 ATAATATATAATATAAAAGAAACATATAATATA
2506694 ATAATATATAA-ATAA
1 ATAATATATAATATAA
2506709 TGATGTAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
31 25 0.61
32 4 0.10
33 12 0.29
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (33 bp):
ATAATATATAATATAAAAGAAACATATAATATA
Found at i:2506808 original size:18 final size:18
Alignment explanation
Indices: 2506568--2506808 Score: 98
Period size: 18 Copynumber: 13.3 Consensus size: 18
2506558 CTTTAATGAT
*
2506568 AATAATATAT-AGATAAA
1 AATAATATATAATATAAA
*
2506585 AAT-GTATAATAATATAAA
1 AATAATAT-ATAATATAAA
*
2506603 AATGACT-TAATAATATATAA
1 AAT-AATAT-ATAATATA-AA
2506623 AATAAT-TATAATATATAA
1 AATAATATATAATATA-AA
* * *
2506641 TATAAAAGCA-ATATATAAA
1 AATAATA-TATA-ATATAAA
*
2506660 AATAATATATAATAT-AT
1 AATAATATATAATATAAA
* *
2506677 AATAAACATATAATATAAT
1 AAT-AATATATAATATAAA
* *
2506696 AATATATAAATAATGATGTAA
1 AATA-ATATATAAT-AT-AAA
* *
2506717 AATAATA-AT-TTGTGAAA
1 AATAATATATAATAT-AAA
2506734 AATAATATAT-A-AT--A
1 AATAATATATAATATAAA
2506748 AATAATA-ATAATAT--A
1 AATAATATATAATATAAA
*
2506763 AATAATATATAATAAAATA
1 AATAATATATAATATAA-A
2506782 ATTTTATAATATATAATATAAA
1 A----ATAATATATAATATAAA
2506804 AATAA
1 AATAA
2506809 GGTTAAAAAT
Statistics
Matches: 176, Mismatches: 23, Indels: 49
0.71 0.09 0.20
Matches are distributed among these distances:
13 2 0.01
14 9 0.05
15 10 0.06
16 9 0.05
17 21 0.12
18 48 0.27
19 38 0.22
20 17 0.10
21 5 0.03
22 2 0.01
23 15 0.09
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.34
Consensus pattern (18 bp):
AATAATATATAATATAAA
Found at i:2525381 original size:54 final size:54
Alignment explanation
Indices: 2525317--2525424 Score: 162
Period size: 54 Copynumber: 2.0 Consensus size: 54
2525307 GGTTCTAAAG
* * * *
2525317 AAGACCATATCGTGTAAGATCATAACTGGTGGGTTATGGCATCATATGGAAAAA
1 AAGACCATATCATGTAAGACCATAACTAGTAGGTTATGGCATCATATGGAAAAA
* *
2525371 AAGACTATATCATGTAAGACCGTAACTAGTAGGTTATGGCATCATATGGAAAAA
1 AAGACCATATCATGTAAGACCATAACTAGTAGGTTATGGCATCATATGGAAAAA
2525425 TTTTAAAAAG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (54 bp):
AAGACCATATCATGTAAGACCATAACTAGTAGGTTATGGCATCATATGGAAAAA
Found at i:2525663 original size:31 final size:27
Alignment explanation
Indices: 2525590--2525668 Score: 95
Period size: 28 Copynumber: 2.7 Consensus size: 27
2525580 GGAAAACCTT
2525590 TAAAAGGACACCTTTGTGGCGAGATTA
1 TAAAAGGACACCTTTGTGGCGAGATTA
*
2525617 TAAAAGGAAAGCCTTTGTGGCGAGTACTTAA
1 TAAAAGGACA-CCTTTGTGGCGAG-A-TT-A
*
2525648 TAAAAATGACACCTTTGTGGC
1 T-AAAAGGACACCTTTGTGGC
2525669 AATCATTGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
27 9 0.20
28 13 0.30
29 1 0.02
30 2 0.05
31 12 0.27
32 7 0.16
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (27 bp):
TAAAAGGACACCTTTGTGGCGAGATTA
Found at i:2537768 original size:18 final size:18
Alignment explanation
Indices: 2537745--2537800 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
2537735 CTACTAAAGT
2537745 AGCTTGAGTCTTCGAAGG
1 AGCTTGAGTCTTCGAAGG
*
2537763 AGCTT--G-C--CGGAAGT
1 AGCTTGAGTCTTC-GAAGG
*
2537777 AGCCTGAGTCTTCGAAGG
1 AGCTTGAGTCTTCGAAGG
2537795 AGCTTG
1 AGCTTG
2537801 TCAGAATGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 12
0.64 0.09 0.27
Matches are distributed among these distances:
13 1 0.04
14 8 0.29
15 1 0.04
16 2 0.07
17 1 0.04
18 14 0.50
19 1 0.04
ACGTcount: A:0.21, C:0.20, G:0.34, T:0.25
Consensus pattern (18 bp):
AGCTTGAGTCTTCGAAGG
Found at i:2538680 original size:61 final size:61
Alignment explanation
Indices: 2538580--2538701 Score: 235
Period size: 61 Copynumber: 2.0 Consensus size: 61
2538570 AGTCAAGCAC
*
2538580 TCATTCATAATTTGGAAGAAGGTACCATGATCCTTACATCCAGGTATTTGAGATGCAAGTA
1 TCATTCATAATTTGGAAGAAGGTACCATGATCCTGACATCCAGGTATTTGAGATGCAAGTA
2538641 TCATTCATAATTTGGAAGAAGGTACCATGATCCTGACATCCAGGTATTTGAGATGCAAGTA
1 TCATTCATAATTTGGAAGAAGGTACCATGATCCTGACATCCAGGTATTTGAGATGCAAGTA
2538702 AACTCTGACT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.30
Consensus pattern (61 bp):
TCATTCATAATTTGGAAGAAGGTACCATGATCCTGACATCCAGGTATTTGAGATGCAAGTA
Found at i:2554110 original size:30 final size:30
Alignment explanation
Indices: 2554076--2554143 Score: 136
Period size: 30 Copynumber: 2.3 Consensus size: 30
2554066 AAAATGTTGT
2554076 GGGAGAAATAATAAAATACTAGTTGATGGG
1 GGGAGAAATAATAAAATACTAGTTGATGGG
2554106 GGGAGAAATAATAAAATACTAGTTGATGGG
1 GGGAGAAATAATAAAATACTAGTTGATGGG
2554136 GGGAGAAA
1 GGGAGAAA
2554144 CAAAAGTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.44, C:0.03, G:0.32, T:0.21
Consensus pattern (30 bp):
GGGAGAAATAATAAAATACTAGTTGATGGG
Found at i:2557082 original size:40 final size:40
Alignment explanation
Indices: 2556844--2557070 Score: 303
Period size: 40 Copynumber: 5.7 Consensus size: 40
2556834 TTGAGAGTTA
* * *
2556844 TATAGCCGGGCTAAGTCCCGAAGAGCATTTGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGT
* *
2556884 TATATACGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGT
* *
2556924 TATATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGT
* * *
2556964 TATA-CCTCGGCTAAGTCTCGAAGAGCATTCGTGCTAGAGT
1 TATATCC-GGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGT
* * * *
2557004 TAGATCAGGGTTAAGTCCCGAAGAGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGT
*
2557044 TATATCCGGGCTAGGTCCCGAAGAGCA
1 TATATCCGGGCTAAGTCCCGAAGAGCA
2557071 ATCATGCTGG
Statistics
Matches: 164, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
39 2 0.01
40 161 0.98
41 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGT
Found at i:2557296 original size:25 final size:25
Alignment explanation
Indices: 2557246--2557296 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
2557236 TGTGTAACAA
* *
2557246 CAAATGAATAGGGGCACTATGTGTG
1 CAAATGAATAGAGGCACTATGAGTG
*
2557271 CAAATGATTAGAGGCACTGA-GAGTG
1 CAAATGAATAGAGGCACT-ATGAGTG
2557296 C
1 C
2557297 GAGTTCTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.33, C:0.14, G:0.31, T:0.22
Consensus pattern (25 bp):
CAAATGAATAGAGGCACTATGAGTG
Found at i:2562727 original size:122 final size:119
Alignment explanation
Indices: 2562513--2562735 Score: 306
Period size: 122 Copynumber: 1.8 Consensus size: 119
2562503 CACAATAACA
*
2562513 ATGAGAATAAGAATAGAAATGTAATGGGTATGAGGTTTTCTAATCTCAATTTAACACAGAATGTA
1 ATGAGAATAAGAATAGAAATGTAATGGGTATGAGGTTTCCTAATCTCAATTTAACACAGAATGTA
*
2562578 TTATAACTAACCTAGAAATACAAATTAAATGATAGACATTGGTATGGTAATAGC
66 TGATAACTAACCTAGAAATACAAATTAAATGATAGACATTGGTATGGTAATAGC
* * * ** *
2562632 ATGAGAATAAGCATAGTAATGTCATGGGTATGAGGTGTTCCTAATAACTTGATTTAACA-TGAAA
1 ATGAGAATAAGAATAGAAATGTAATGGGTATGAGGT-TTCCTAAT--CTCAATTTAACACAG-AA
*
2562696 TGTATGATAACTAACCTA-AGAATGCAAATTAAATGATAGA
62 TGTATGATAACTAACCTAGA-AATACAAATTAAATGATAGA
2562736 AAAATGAAAA
Statistics
Matches: 90, Mismatches: 9, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
119 33 0.37
120 7 0.08
121 2 0.02
122 48 0.53
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.30
Consensus pattern (119 bp):
ATGAGAATAAGAATAGAAATGTAATGGGTATGAGGTTTCCTAATCTCAATTTAACACAGAATGTA
TGATAACTAACCTAGAAATACAAATTAAATGATAGACATTGGTATGGTAATAGC
Found at i:2565837 original size:234 final size:234
Alignment explanation
Indices: 2565428--2565895 Score: 900
Period size: 234 Copynumber: 2.0 Consensus size: 234
2565418 CATAGGTGTC
2565428 TATCCGCATCTACGTAATTACCTTTGATTCAGAATATCACAGAGTTTCACATCCTCACTAAAGAT
1 TATCCGCATCTACGTAATTACCTTTGATTCAGAATATCACAGAGTTTCACATCCTCACTAAAGAT
2565493 TCACTCAAATCAATCCAGGTGTTTAAGGACAATAAATGAAGCACTCAATAATCAATAATAAAAAG
66 TCACTCAAATCAATCCAGGTGTTTAAGGACAATAAATGAAGCACTCAATAATCAATAATAAAAAG
2565558 TCATTACCATAGGCTTGCATGAAAATCAAATCTCCACCACTATAATTTAAGATGATACATCAATC
131 TCATTACCATAGGCTTGCATGAAAATCAAATCTCCACCACTATAATTTAAGATGATACATCAATC
* * **
2565623 AAAAGGTCTTTAGAGGGTTGTAGTGCTGCTTGGTTAGGG
196 AAAAGGTCTTTAGAAGGTTGTAATGAGGCTTGGTTAGGG
2565662 TATCCGCATCTACGTAATTACCTTTGATTCAGAATATCACAGAGTTTCACATCCTCACTAAAGAT
1 TATCCGCATCTACGTAATTACCTTTGATTCAGAATATCACAGAGTTTCACATCCTCACTAAAGAT
2565727 TCACTCAAATCAATCCAGGTGTTTAAGGACAATAAATGAAGCACTCAATAATCAATAATAAAAAG
66 TCACTCAAATCAATCCAGGTGTTTAAGGACAATAAATGAAGCACTCAATAATCAATAATAAAAAG
2565792 TCATTACCATAGGCTTGCATGAAAATCAAATCTCCACCACTATAATTTAAGATGATACATCAATC
131 TCATTACCATAGGCTTGCATGAAAATCAAATCTCCACCACTATAATTTAAGATGATACATCAATC
2565857 AAAAGGTCTTTAGAAGGTTGTAATGAGGCTTGGTTAGGG
196 AAAAGGTCTTTAGAAGGTTGTAATGAGGCTTGGTTAGGG
2565896 GGTGTGGTCA
Statistics
Matches: 230, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
234 230 1.00
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (234 bp):
TATCCGCATCTACGTAATTACCTTTGATTCAGAATATCACAGAGTTTCACATCCTCACTAAAGAT
TCACTCAAATCAATCCAGGTGTTTAAGGACAATAAATGAAGCACTCAATAATCAATAATAAAAAG
TCATTACCATAGGCTTGCATGAAAATCAAATCTCCACCACTATAATTTAAGATGATACATCAATC
AAAAGGTCTTTAGAAGGTTGTAATGAGGCTTGGTTAGGG
Found at i:2575573 original size:13 final size:13
Alignment explanation
Indices: 2575555--2575580 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2575545 GTTGTTTATT
2575555 AACTAATTAACTA
1 AACTAATTAACTA
2575568 AACTAATTAACTA
1 AACTAATTAACTA
2575581 GCTAAACTAA
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:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
AACTAATTAACTA
Found at i:2577207 original size:38 final size:38
Alignment explanation
Indices: 2577163--2577320 Score: 169
Period size: 38 Copynumber: 4.1 Consensus size: 38
2577153 TTTAAACTTA
* *
2577163 GATATAATACCAGCAGTAGGCCTGCGAGATTTAACCCG
1 GATATAATACCAGCAGTAAGCCTGCGGGATTTAACCCG
* *
2577201 GATATAATAACAGCACG-AAGCCTACGGGATTTAACCCG
1 GATATAATACCAGCA-GTAAGCCTGCGGGATTTAACCCG
* * *
2577239 AATATAATACCAAC-GTGAAGCCTGCGGGATTTAACCCA
1 GATATAATACCAGCAGT-AAGCCTGCGGGATTTAACCCG
* *
2577277 GATATAATTCCAGCA-TATAGCCTGCGGGTCTTTAAGCCCG
1 GATATAATACCAGCAGTA-AGCCTGCGGG-ATTTAA-CCCG
2577317 GATA
1 GATA
2577321 CACATCAAAT
Statistics
Matches: 99, Mismatches: 14, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
36 1 0.01
37 1 0.01
38 84 0.85
39 6 0.06
40 7 0.07
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.22
Consensus pattern (38 bp):
GATATAATACCAGCAGTAAGCCTGCGGGATTTAACCCG
Found at i:2577291 original size:76 final size:78
Alignment explanation
Indices: 2577126--2577291 Score: 203
Period size: 76 Copynumber: 2.2 Consensus size: 78
2577116 AAACCCGAAC
* * ** * *
2577126 ATAACACCAGCACGAAGCTTACGGGACTTTAAACTTAGATATAATACCAGCAGTAGGCCTGCGAG
1 ATAATACCAGCACGAAGCCTACGGGACTTTAAACCGAGATATAATACCAACAGTAAGCCTGCGAG
*
2577191 ATTTAACCCGGAT
66 ATTTAACCCAGAT
* * *
2577204 ATAATAACAGCACGAAGCCTACGGGA-TTTAACCCGA-ATATAATACCAAC-GTGAAGCCTGCGG
1 ATAATACCAGCACGAAGCCTACGGGACTTTAAACCGAGATATAATACCAACAGT-AAGCCTGCGA
2577266 GATTTAACCCAGAT
65 GATTTAACCCAGAT
*
2577280 ATAATTCCAGCA
1 ATAATACCAGCA
2577292 TATAGCCTGC
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
75 2 0.03
76 43 0.57
77 7 0.09
78 23 0.31
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (78 bp):
ATAATACCAGCACGAAGCCTACGGGACTTTAAACCGAGATATAATACCAACAGTAAGCCTGCGAG
ATTTAACCCAGAT
Found at i:2590609 original size:40 final size:40
Alignment explanation
Indices: 2590515--2590739 Score: 233
Period size: 40 Copynumber: 5.6 Consensus size: 40
2590505 TATTCGAATG
* *
2590515 ATATCCGGGCTAAG-TCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTA-GCGACT
* * * *
2590556 ATAACCGGACTAAGATCCGAAGGCATTCGTG-TGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCT-AG-CGACT
* *
2590596 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGCGACT
* * *
2590636 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGCGACA
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGCGACT
* * *
2590676 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
* *
2590716 ACATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGATCCGAAGGC
2590740 CTTGCGCAAG
Statistics
Matches: 157, Mismatches: 20, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
39 1 0.01
40 126 0.80
41 29 0.18
42 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGCGACT
Found at i:2590695 original size:80 final size:80
Alignment explanation
Indices: 2590515--2590739 Score: 283
Period size: 80 Copynumber: 2.8 Consensus size: 80
2590505 TATTCGAATG
* * * *
2590515 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACTATAACCGGACTAAGATCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTA-GTGACTATATCCGGGCTAAGACCCGAAGGC
* *
2590580 ATTCGTGTGAGTTGCT
65 ATTCGTGTGAGTCGCA
* * * *
2590596 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATTATATCCGGGCTAAAACCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
*
2590661 TTTGTGCT-AG-CGACA
66 TTCGTG-TGAGTCG-CA
* * *
2590676 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACCACATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGC
2590740 CTTGCGCAAG
Statistics
Matches: 124, Mismatches: 18, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
79 1 0.01
80 90 0.73
81 33 0.27
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (80 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
TTCGTGTGAGTCGCA
Found at i:2590733 original size:120 final size:121
Alignment explanation
Indices: 2590515--2590739 Score: 296
Period size: 120 Copynumber: 1.9 Consensus size: 121
2590505 TATTCGAATG
** * * *
2590515 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACTATAACCGGACTAAGATCCGAAGGC
1 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGGCGACAATAACCGGACTAAGATCCGAAGGC
* * *
2590580 ATTCGTGTGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
66 ATTCATGTGAGTTGCCACATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
* *
2590636 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTA-GCGACAATATCCGGGCTAAG-TCCCGAAGG
1 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGGCGACAATAACCGGACTAAGAT-CCGAAGG
*
2590699 CATTTATGCT-AG-TGACCACATCCGGGCTAAGACCCGAAGGC
65 CATTCATG-TGAGTTG-CCACATCCGGGCTAAGACCCGAAGGC
2590740 CTTGCGCAAG
Statistics
Matches: 90, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
119 3 0.03
120 55 0.61
121 32 0.36
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (121 bp):
ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGGCGACAATAACCGGACTAAGATCCGAAGGC
ATTCATGTGAGTTGCCACATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
Found at i:2592388 original size:27 final size:27
Alignment explanation
Indices: 2592358--2592535 Score: 137
Period size: 27 Copynumber: 6.6 Consensus size: 27
2592348 ATATTGAGCC
* *
2592358 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * * *
2592385 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
2592412 CGCACACTTAGTGCTACATAGTCAAACC
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
2592440 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
2592467 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
2592494 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTACATAA-TCA-ACT
2592521 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
2592536 GTACAATTTA
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 96 0.79
28 23 0.19
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:2592470 original size:55 final size:54
Alignment explanation
Indices: 2592358--2592535 Score: 164
Period size: 54 Copynumber: 3.3 Consensus size: 54
2592348 ATATTGAGCC
* * * * *
2592358 CGCACACTCAGTGCTATATAATCAACTCGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
* * ** *
2592412 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACCCGCACACTTAGTGCCACATAATCAAAT
* *** *
2592467 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTA-CATAATCAACCCGCACACTTAGTGCCACATAA-TCA-AAT
2592521 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
2592536 GTACAATTTA
Statistics
Matches: 100, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
53 1 0.01
54 55 0.55
55 44 0.44
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
Found at i:2600394 original size:27 final size:27
Alignment explanation
Indices: 2600364--2600541 Score: 137
Period size: 27 Copynumber: 6.6 Consensus size: 27
2600354 ATATTGAGCC
* * *
2600364 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAAAT
* * *
2600391 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
* *
2600418 CGCACACTTAGTGCTACATAGTCAAACC
1 CGCACACTTAGTGCTACATAATCAAA-T
* ** ** *
2600446 CTCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAAAT
* **
2600473 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAAAT
*
2600500 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTACATAA-TCA-AAT
2600527 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
2600542 GTACAATTTA
Statistics
Matches: 120, Mismatches: 26, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
26 2 0.02
27 96 0.80
28 22 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAAAT
Found at i:2601874 original size:87 final size:88
Alignment explanation
Indices: 2601720--2601896 Score: 338
Period size: 87 Copynumber: 2.0 Consensus size: 88
2601710 TTCCTCTATT
2601720 CGGCCAAGGATGTTTAAGAATGAACTCTTTTTTTTTTTTTTGTTTTCTTTCTTCAATTCACGGCA
1 CGGCCAAGGATGTTTAAGAATGAACTC-TTTTTTTTTTTTTGTTTTCTTTCTTCAATTCACGGCA
2601785 ACAAGGGGGGGGTGAGACCATGTA
65 ACAAGGGGGGGGTGAGACCATGTA
2601809 CGGCCAAGGATGTTTAAGAATGAACTC-TTTTTTTTTTTTGTTTTCTTTCTTCAATTCACGGCAA
1 CGGCCAAGGATGTTTAAGAATGAACTCTTTTTTTTTTTTTGTTTTCTTTCTTCAATTCACGGCAA
2601873 CAAGGGGGGGGTGAGACCATGTA
66 CAAGGGGGGGGTGAGACCATGTA
2601896 C
1 C
2601897 TTTTTTTTTT
Statistics
Matches: 88, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
87 61 0.69
89 27 0.31
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.37
Consensus pattern (88 bp):
CGGCCAAGGATGTTTAAGAATGAACTCTTTTTTTTTTTTTGTTTTCTTTCTTCAATTCACGGCAA
CAAGGGGGGGGTGAGACCATGTA
Found at i:2603211 original size:13 final size:13
Alignment explanation
Indices: 2603193--2603218 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2603183 ACCTGAAAGC
2603193 AATTTAATTCATA
1 AATTTAATTCATA
2603206 AATTTAATTCATA
1 AATTTAATTCATA
2603219 TTAGGACACA
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:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTTAATTCATA
Found at i:2603633 original size:20 final size:21
Alignment explanation
Indices: 2603608--2603646 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2603598 TCAAACAAGA
2603608 AAATGAGCTCAA-TGAGCTGG
1 AAATGAGCTCAATTGAGCTGG
*
2603628 AAATGAGCTGAATTGAGCT
1 AAATGAGCTCAATTGAGCT
2603647 CAACGAGCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.23
Consensus pattern (21 bp):
AAATGAGCTCAATTGAGCTGG
Found at i:2603932 original size:66 final size:66
Alignment explanation
Indices: 2603850--2604020 Score: 342
Period size: 66 Copynumber: 2.6 Consensus size: 66
2603840 TACACTGAAT
2603850 CCTTTAACATAACCAACTTGAAATCCAAATATCTCAATCGATTCTAATGTTCTCATGTAGCCGAA
1 CCTTTAACATAACCAACTTGAAATCCAAATATCTCAATCGATTCTAATGTTCTCATGTAGCCGAA
2603915 A
66 A
2603916 CCTTTAACATAACCAACTTGAAATCCAAATATCTCAATCGATTCTAATGTTCTCATGTAGCCGAA
1 CCTTTAACATAACCAACTTGAAATCCAAATATCTCAATCGATTCTAATGTTCTCATGTAGCCGAA
2603981 A
66 A
2603982 CCTTTAACATAACCAACTTGAAATCCAAATATCTCAATC
1 CCTTTAACATAACCAACTTGAAATCCAAATATCTCAATC
2604021 TACACTGAAT
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 105 1.00
ACGTcount: A:0.37, C:0.25, G:0.08, T:0.30
Consensus pattern (66 bp):
CCTTTAACATAACCAACTTGAAATCCAAATATCTCAATCGATTCTAATGTTCTCATGTAGCCGAA
A
Found at i:2606018 original size:23 final size:23
Alignment explanation
Indices: 2605988--2606080 Score: 91
Period size: 23 Copynumber: 4.0 Consensus size: 23
2605978 ATCGAAATAG
*
2605988 AGCCTTTGTGGCGTATTTTGATT
1 AGCCTTTGTGGCGTATTCTGATT
* **
2606011 AGACTTTGTGGCACATTCTGATT
1 AGCCTTTGTGGCGTATTCTGATT
*
2606034 AGCCTTTGT-GCTGTACTCTGATT
1 AGCCTTTGTGGC-GTATTCTGATT
* *
2606057 AGCCTGTT-TGGTGTATTTTGATT
1 AGCCT-TTGTGGCGTATTCTGATT
2606080 A
1 A
2606081 ACCTCTTTTG
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
22 2 0.04
23 51 0.91
24 3 0.05
ACGTcount: A:0.16, C:0.15, G:0.24, T:0.45
Consensus pattern (23 bp):
AGCCTTTGTGGCGTATTCTGATT
Found at i:2608023 original size:48 final size:48
Alignment explanation
Indices: 2607959--2608051 Score: 116
Period size: 48 Copynumber: 1.9 Consensus size: 48
2607949 ACACCATATG
* * *
2607959 TGGACAAACCAGCACATAAATGCCGATAAACGACCAGATAA-CACATTA
1 TGGACAAACCACCACATAAATACCGAT-AACGACCACATAATCACATTA
* * *
2608007 TGGACAAGCCACCACATAATTATCGATAACGACCACATAATCACA
1 TGGACAAACCACCACATAAATACCGATAACGACCACATAATCACA
2608052 GATAAGCTAC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
47 12 0.32
48 26 0.68
ACGTcount: A:0.44, C:0.27, G:0.13, T:0.16
Consensus pattern (48 bp):
TGGACAAACCACCACATAAATACCGATAACGACCACATAATCACATTA
Found at i:2608029 original size:22 final size:21
Alignment explanation
Indices: 2608003--2608047 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2607993 CAGATAACAC
*
2608003 ATTATGGACAAGCCACCACATA
1 ATTATCGACAA-CCACCACATA
* *
2608025 ATTATCGATAACGACCACATA
1 ATTATCGACAACCACCACATA
2608046 AT
1 AT
2608048 CACAGATAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.42, C:0.24, G:0.11, T:0.22
Consensus pattern (21 bp):
ATTATCGACAACCACCACATA
Found at i:2608066 original size:22 final size:22
Alignment explanation
Indices: 2608012--2608068 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
2608002 CATTATGGAC
*
2608012 AAGCCACCACATAATTATCGAT
1 AAGCCACCACATAATCATCGAT
*
2608034 AA-CGACCACATAATCA-CAGAT
1 AAGCCACCACATAATCATC-GAT
*
2608055 AAGCTACCACATAA
1 AAGCCACCACATAA
2608069 CTTCCACCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 1 0.03
21 17 0.57
22 12 0.40
ACGTcount: A:0.46, C:0.28, G:0.09, T:0.18
Consensus pattern (22 bp):
AAGCCACCACATAATCATCGAT
Found at i:2611497 original size:13 final size:13
Alignment explanation
Indices: 2611479--2611504 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2611469 ATACGTGGAA
2611479 CACATGGCCATGT
1 CACATGGCCATGT
2611492 CACATGGCCATGT
1 CACATGGCCATGT
2611505 GTCATACACG
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:0.23, C:0.31, G:0.23, T:0.23
Consensus pattern (13 bp):
CACATGGCCATGT
Found at i:2613096 original size:13 final size:13
Alignment explanation
Indices: 2613071--2613110 Score: 62
Period size: 15 Copynumber: 2.9 Consensus size: 13
2613061 GGATAACAAG
2613071 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
2613084 TTTCGTGAAAAAAAA
1 -TT-GTGAAAAAAAA
2613099 TTGTGAAAAAAA
1 TTGTGAAAAAAA
2613111 GAAGCTAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 10 0.40
14 4 0.16
15 11 0.44
ACGTcount: A:0.57, C:0.03, G:0.15, T:0.25
Consensus pattern (13 bp):
TTGTGAAAAAAAA
Found at i:2615347 original size:68 final size:68
Alignment explanation
Indices: 2615264--2615399 Score: 263
Period size: 68 Copynumber: 2.0 Consensus size: 68
2615254 CTTCTTAATT
2615264 GATCTAGTTCCTAGGATTATTTACTGATGCATAAATTAAGTTCTTTAAATTATGCTTCTTTAATT
1 GATCTAGTTCCTAGGATTATTTACTGATGCATAAATTAAGTTCTTTAAATTATGCTTCTTTAATT
2615329 AAA
66 AAA
*
2615332 GATCTAGTTCCTAGGATTATTTATTGATGCATAAATTAAGTTCTTTAAATTATGCTTCTTTAATT
1 GATCTAGTTCCTAGGATTATTTACTGATGCATAAATTAAGTTCTTTAAATTATGCTTCTTTAATT
2615397 AAA
66 AAA
2615400 CTTTTTGCTG
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (68 bp):
GATCTAGTTCCTAGGATTATTTACTGATGCATAAATTAAGTTCTTTAAATTATGCTTCTTTAATT
AAA
Found at i:2615384 original size:33 final size:33
Alignment explanation
Indices: 2615279--2615384 Score: 76
Period size: 33 Copynumber: 3.2 Consensus size: 33
2615269 AGTTCCTAGG
*
2615279 ATTATTTACTGATGCATAAATTAAGTTCTTTAA
1 ATTATTTATTGATGCATAAATTAAGTTCTTTAA
* * * * *
2615312 ATTATGCTTCTTTAAT-TA-AAGATCT-AGTTC-CTAGG
1 ATTAT--TT-ATTGATGCATAA-AT-TAAGTTCTTTA-A
2615347 ATTATTTATTGATGCATAAATTAAGTTCTTTAA
1 ATTATTTATTGATGCATAAATTAAGTTCTTTAA
2615380 ATTAT
1 ATTAT
2615385 GCTTCTTTAA
Statistics
Matches: 52, Mismatches: 11, Indels: 20
0.63 0.13 0.24
Matches are distributed among these distances:
32 5 0.10
33 20 0.38
34 8 0.15
35 15 0.29
36 4 0.08
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.46
Consensus pattern (33 bp):
ATTATTTATTGATGCATAAATTAAGTTCTTTAA
Found at i:2621544 original size:24 final size:25
Alignment explanation
Indices: 2621517--2621596 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 25
2621507 GTACATGTAT
* *
2621517 GCTCATTCGAGCTG-TTAATGGTAA
1 GCTCATTCGAGCTGAATAACGGTAA
*
2621541 GCTC-CTCTGAGCTGAATAACGGTAA
1 GCTCATTC-GAGCTGAATAACGGTAA
* * * *
2621566 GCTCATACGAGTTGAGTATCGGTAA
1 GCTCATTCGAGCTGAATAACGGTAA
2621591 GCTCAT
1 GCTCAT
2621597 AAGAGTTGAA
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
23 2 0.04
24 10 0.22
25 32 0.71
26 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (25 bp):
GCTCATTCGAGCTGAATAACGGTAA
Found at i:2626704 original size:20 final size:20
Alignment explanation
Indices: 2626681--2626734 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
2626671 AGTTTTTCCC
*
2626681 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
2626701 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
2626721 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
2626735 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:2626716 original size:30 final size:30
Alignment explanation
Indices: 2626681--2626754 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
2626671 AGTTTTTCCC
2626681 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
2626711 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
2626741 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
2626755 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:2626744 original size:20 final size:20
Alignment explanation
Indices: 2626681--2626745 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
2626671 AGTTTTTCCC
* * * *
2626681 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
2626701 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
2626720 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
2626741 AGCTC
1 AGCTC
2626746 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:2630917 original size:29 final size:29
Alignment explanation
Indices: 2630854--2630921 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
2630844 TAATCAACCG
*
2630854 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
2630883 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
2630912 CGCACACTTA
1 CGCACACTTA
2630922 CCTTTTCCGC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 3 0.09
29 30 0.91
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:2631033 original size:174 final size:174
Alignment explanation
Indices: 2630743--2631070 Score: 629
Period size: 174 Copynumber: 1.9 Consensus size: 174
2630733 AACTCAAGGT
* *
2630743 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCACACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCACACCCTTAATGTAAATAATTTATA
2630808 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
2630873 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
*
2630917 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCACACCCTTAATGTAAATAATTTATA
2630982 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
2631047 ACTTTAAACTCACACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
2631071 TGTACAATTT
Statistics
Matches: 151, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
174 151 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCACACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:2631064 original size:29 final size:30
Alignment explanation
Indices: 2631030--2631101 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
2631020 ATCAACCGCG
*
2631030 CACACTTAGTGCCATGTAC-TTTAAACTCA
1 CACACTTAGTGCCATGTACATTTAAACCCA
*
2631059 CACACTTAGTG-C-TGTACAATTTAAACCCG
1 CACACTTAGTGCCATGTAC-ATTTAAACCCA
2631088 CACACTTAGTGCCA
1 CACACTTAGTGCCA
2631102 ATCTCATGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
27 5 0.14
28 1 0.03
29 30 0.81
30 1 0.03
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.28
Consensus pattern (30 bp):
CACACTTAGTGCCATGTACATTTAAACCCA
Found at i:2633187 original size:15 final size:16
Alignment explanation
Indices: 2633162--2633214 Score: 69
Period size: 15 Copynumber: 3.5 Consensus size: 16
2633152 ACTTTATCCA
2633162 TCATC-CATCATCC-C
1 TCATCTCATCATCCTC
2633176 TCATCTCATCATCCCTC
1 TCATCTCATCAT-CCTC
2633193 TCATCTC-TCATCCTC
1 TCATCTCATCATCCTC
2633208 TC-TCTCA
1 TCATCTCA
2633215 ACTCTCTTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
14 9 0.26
15 12 0.34
16 6 0.17
17 8 0.23
ACGTcount: A:0.17, C:0.47, G:0.00, T:0.36
Consensus pattern (16 bp):
TCATCTCATCATCCTC
Found at i:2633201 original size:19 final size:19
Alignment explanation
Indices: 2633179--2633220 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2633169 TCATCCCTCA
*
2633179 TCTCATCATCCCTCTCATC
1 TCTCATCATCCCTCTCAAC
* *
2633198 TCTCATCCTCTCTCTCAAC
1 TCTCATCATCCCTCTCAAC
2633217 TCTC
1 TCTC
2633221 TTAGCTCTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.14, C:0.48, G:0.00, T:0.38
Consensus pattern (19 bp):
TCTCATCATCCCTCTCAAC
Found at i:2654861 original size:9 final size:9
Alignment explanation
Indices: 2654847--2654872 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2654837 TAATGTTTTA
2654847 TTACCTTTC
1 TTACCTTTC
2654856 TTACCTTTC
1 TTACCTTTC
2654865 TTACCTTT
1 TTACCTTT
2654873 TAGCACTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.31, G:0.00, T:0.58
Consensus pattern (9 bp):
TTACCTTTC
Found at i:2656653 original size:4 final size:4
Alignment explanation
Indices: 2656644--2656680 Score: 56
Period size: 4 Copynumber: 9.0 Consensus size: 4
2656634 CAAATAAAAG
*
2656644 AAAT AAAT AAAT AAAT AAGAT AAAT AAAT CAAT AAAT
1 AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT
2656681 CAAAGATTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:2656657 original size:17 final size:17
Alignment explanation
Indices: 2656635--2656679 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
2656625 AATCCAAGTC
2656635 AAATAAA-AGAAATAAAT
1 AAATAAATA-AAATAAAT
*
2656652 AAATAAATAAGATAAAT
1 AAATAAATAAAATAAAT
*
2656669 AAATCAATAAA
1 AAATAAATAAA
2656680 TCAAAGATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 23 0.96
18 1 0.04
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.20
Consensus pattern (17 bp):
AAATAAATAAAATAAAT
Found at i:2662235 original size:13 final size:14
Alignment explanation
Indices: 2662217--2662249 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2662207 CTTTTTCTAC
*
2662217 TCTTTTTG-CTTTT
1 TCTTTTTGTATTTT
2662230 TCTTTTTGTATTTT
1 TCTTTTTGTATTTT
2662244 TCTTTT
1 TCTTTT
2662250 ATTTGACACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.03, C:0.12, G:0.06, T:0.79
Consensus pattern (14 bp):
TCTTTTTGTATTTT
Found at i:2662605 original size:7 final size:8
Alignment explanation
Indices: 2662582--2662611 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
2662572 AAATTATATC
2662582 AATCAAAA
1 AATCAAAA
2662590 AATCAAAA
1 AATCAAAA
2662598 AATCAAAA
1 AATCAAAA
*
2662606 ATTCAA
1 AATCAA
2662612 CAATTTATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.70, C:0.13, G:0.00, T:0.17
Consensus pattern (8 bp):
AATCAAAA
Found at i:2665210 original size:20 final size:20
Alignment explanation
Indices: 2665185--2665224 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2665175 TACCAAAATC
2665185 GCTTGAAAAGTTTTGACATT
1 GCTTGAAAAGTTTTGACATT
2665205 GCTTGAAAAGTTTTGACATT
1 GCTTGAAAAGTTTTGACATT
2665225 AGAGGCATTT
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:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (20 bp):
GCTTGAAAAGTTTTGACATT
Found at i:2666817 original size:51 final size:50
Alignment explanation
Indices: 2666754--2666879 Score: 162
Period size: 51 Copynumber: 2.5 Consensus size: 50
2666744 ATGAACAAAT
* *
2666754 GAGTTACTTAATGCATGACTTCATTTAAGATGCAAACATTAACTATCATGA
1 GAGTTACATAATGCATGACTTCATTTAAGATGCAAAC-TTAACTAACATGA
* * * *
2666805 GAGTTACATAATGCATGTCATAATTTATGATGCAAACTTAACTAACATGA
1 GAGTTACATAATGCATGACTTCATTTAAGATGCAAACTTAACTAACATGA
* * *
2666855 GAGTTTCATAATTCATGAATTCATT
1 GAGTTACATAATGCATGACTTCATT
2666880 AAACGCAAAA
Statistics
Matches: 63, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
50 31 0.49
51 32 0.51
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.35
Consensus pattern (50 bp):
GAGTTACATAATGCATGACTTCATTTAAGATGCAAACTTAACTAACATGA
Found at i:2670955 original size:51 final size:50
Alignment explanation
Indices: 2670897--2671080 Score: 185
Period size: 51 Copynumber: 3.6 Consensus size: 50
2670887 TCGGTTCACA
*
2670897 TAGTAGCCTGCACATAGTACTACACATGTGACAATTACCA-CCCGATACATG
1 TAGTAGCCTGCACATAGTACTACACATGTGACAA-TACCATCCCG-TACACG
* * * * * *
2670948 TAGTAGCCTGCACATATTACTACACACGTGATCGAA-ACTATCCTGTACGCA
1 TAGTAGCCTGCACATAGTACTACACATGTGA-C-AATACCATCCCGTACACG
* * * * *
2670999 TAGTAGCCTGCACATAGTACTACACATGCGAC-CTATCATTTCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACAATACCA-TCCCGTACACG
*
2671049 TAGTAGCATGCACATAGTACTACACATGTGAC
1 TAGTAGCCTGCACATAGTACTACACATGTGAC
2671081 CATCGTACAC
Statistics
Matches: 109, Mismatches: 19, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
49 2 0.02
50 38 0.35
51 63 0.58
52 4 0.04
53 2 0.02
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACAATACCATCCCGTACACG
Found at i:2685500 original size:27 final size:26
Alignment explanation
Indices: 2685452--2685535 Score: 60
Period size: 27 Copynumber: 3.1 Consensus size: 26
2685442 TTATGACCCT
* * *
2685452 TTTCAATCTCAATCTCTCTTTCCTTTC
1 TTTCACTCTC-ATTTCTTTTTCCTTTC
* *
2685479 TTTCACTCTCTTTTTCTTTTTCAATTTC
1 TTTCACTCTC-ATTTCTTTTTC-CTTTC
** *
2685507 TTTTTCTCTCATTTCTTTTTTCTTCTC
1 TTTCACTCTCATTTCTTTTTCCTT-TC
2685534 TT
1 TT
2685536 AAATTCTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
26 2 0.05
27 30 0.68
28 12 0.27
ACGTcount: A:0.10, C:0.27, G:0.00, T:0.63
Consensus pattern (26 bp):
TTTCACTCTCATTTCTTTTTCCTTTC
Found at i:2686244 original size:25 final size:25
Alignment explanation
Indices: 2686210--2686260 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
2686200 GTTAGGACCT
2686210 GAATAAGGAACACTTCCAACAGTCA
1 GAATAAGGAACACTTCCAACAGTCA
2686235 GAATAAGGAACACTTCCAACAGTCA
1 GAATAAGGAACACTTCCAACAGTCA
2686260 G
1 G
2686261 TTAGAAGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (25 bp):
GAATAAGGAACACTTCCAACAGTCA
Found at i:2687765 original size:51 final size:50
Alignment explanation
Indices: 2687688--2687807 Score: 141
Period size: 51 Copynumber: 2.4 Consensus size: 50
2687678 ATGAACAAAT
* * * * *
2687688 GAGTTACTTAATGCATGACTTCATTTAAGATGCAAACATTAACTATCATGA
1 GAGTTACATAATGCATGACATAATTTAAGATGCAAAC-TTAACTACCATAA
* * *
2687739 GAGTTACATAATGCATGTCATAATTTATGATGCAATCTTAACTACCATAA
1 GAGTTACATAATGCATGACATAATTTAAGATGCAAACTTAACTACCATAA
* *
2687789 GAGTTTCATAATTCATGAC
1 GAGTTACATAATGCATGAC
2687808 TTCATTAAAT
Statistics
Matches: 58, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
50 27 0.47
51 31 0.53
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (50 bp):
GAGTTACATAATGCATGACATAATTTAAGATGCAAACTTAACTACCATAA
Found at i:2687861 original size:25 final size:25
Alignment explanation
Indices: 2687833--2687880 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
2687823 ACACATTATG
2687833 CATATCATAATTAAAAGATGCAATT
1 CATATCATAATTAAAAGATGCAATT
*
2687858 CATATTATAATTAAAAGATGCAA
1 CATATCATAATTAAAAGATGCAA
2687881 ACACTTAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.31
Consensus pattern (25 bp):
CATATCATAATTAAAAGATGCAATT
Found at i:2688558 original size:38 final size:38
Alignment explanation
Indices: 2688514--2688589 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
2688504 AACAAAAAGT
*
2688514 TTAGGAAAAACATACAAAAATTGGAAAACAAGGGTCAC
1 TTAGGAAAAACATACAAAAATTAGAAAACAAGGGTCAC
*
2688552 TTAGGAAAAACATGCAAAAATTAGAAAACAAGGGTCAC
1 TTAGGAAAAACATACAAAAATTAGAAAACAAGGGTCAC
2688590 ACGGCCGTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.53, C:0.13, G:0.18, T:0.16
Consensus pattern (38 bp):
TTAGGAAAAACATACAAAAATTAGAAAACAAGGGTCAC
Found at i:2690119 original size:20 final size:21
Alignment explanation
Indices: 2690096--2690140 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
2690086 CATAACAGAA
**
2690096 GCACCAAA-GTGCTGACAGGG
1 GCACCAAATGTGCAAACAGGG
2690116 GCA-CAAATGTGCAAACAGGG
1 GCACCAAATGTGCAAACAGGG
2690136 GCACC
1 GCACC
2690141 GTAGTGTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 4 0.19
20 16 0.76
21 1 0.05
ACGTcount: A:0.33, C:0.27, G:0.31, T:0.09
Consensus pattern (21 bp):
GCACCAAATGTGCAAACAGGG
Found at i:2690195 original size:20 final size:20
Alignment explanation
Indices: 2690172--2690210 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2690162 AAGTGTATAT
*
2690172 AGAGGCACCGAAGTGCAAAC
1 AGAGACACCGAAGTGCAAAC
*
2690192 AGAGACACTGAAGTGCAAA
1 AGAGACACCGAAGTGCAAA
2690211 TCCCGTACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.21, G:0.28, T:0.08
Consensus pattern (20 bp):
AGAGACACCGAAGTGCAAAC
Found at i:2709269 original size:29 final size:29
Alignment explanation
Indices: 2709226--2709424 Score: 193
Period size: 29 Copynumber: 6.8 Consensus size: 29
2709216 TATCAACGAG
* *
2709226 CATCGATTAATGAAAAGGAATGGTGACAAC
1 CATCGAAT-ATGAAAAGGGATGGTGACAAC
** *
2709256 CATCGAATATGAAAAGGGATGGTTTCGAC
1 CATCGAATATGAAAAGGGATGGTGACAAC
*
2709285 CATTGAATATGAAAAGGGATGGTGA-AGAC
1 CATCGAATATGAAAAGGGATGGTGACA-AC
* * **
2709314 CATCAAATATAAAAAGGGATGGTGACGGC
1 CATCGAATATGAAAAGGGATGGTGACAAC
* **
2709343 CATAGAATATGAAAAGGGATGGTTTCAAC
1 CATCGAATATGAAAAGGGATGGTGACAAC
* **
2709372 CTTCGAATATGAAAAGGGATGGTTTCAAC
1 CATCGAATATGAAAAGGGATGGTGACAAC
* * *
2709401 CATCGATTAAAGAAAATGGATGGT
1 CATCGAAT-ATGAAAAGGGATGGT
2709425 TTCGACCATC
Statistics
Matches: 139, Mismatches: 27, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
29 119 0.86
30 20 0.14
ACGTcount: A:0.40, C:0.12, G:0.26, T:0.23
Consensus pattern (29 bp):
CATCGAATATGAAAAGGGATGGTGACAAC
Found at i:2720215 original size:18 final size:18
Alignment explanation
Indices: 2720192--2720227 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2720182 TTAAAAACTC
2720192 TTTATTCCCTCTATTCCA
1 TTTATTCCCTCTATTCCA
**
2720210 TTTATTCTTTCTATTCCA
1 TTTATTCCCTCTATTCCA
2720228 ATTTCAACCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.28, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTATTCCCTCTATTCCA
Found at i:2722743 original size:9 final size:9
Alignment explanation
Indices: 2722729--2722804 Score: 107
Period size: 9 Copynumber: 8.4 Consensus size: 9
2722719 CTAGTGATTC
2722729 AATTCGGGT
1 AATTCGGGT
*
2722738 AATTCGAGT
1 AATTCGGGT
*
2722747 AATTCGGAT
1 AATTCGGGT
*
2722756 AATTTGGGT
1 AATTCGGGT
2722765 AATTCGGGT
1 AATTCGGGT
*
2722774 AATTCGGTT
1 AATTCGGGT
2722783 AATTCGGGT
1 AATTCGGGT
*
2722792 AATTCGGTT
1 AATTCGGGT
2722801 AATT
1 AATT
2722805 TTTAACCAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 58 1.00
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.38
Consensus pattern (9 bp):
AATTCGGGT
Found at i:2726593 original size:29 final size:28
Alignment explanation
Indices: 2726557--2726634 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
2726547 TCATGAGATT
2726557 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
2726587 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
2726614 TGGCACTAAGTGTGCGTGGTT
1 -GGCACTAAGTGTGCG-GGTT
2726635 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:2726853 original size:175 final size:174
Alignment explanation
Indices: 2726587--2726949 Score: 681
Period size: 175 Copynumber: 2.1 Consensus size: 174
2726577 AAATTGTACA
2726587 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
*
2726652 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACCTTACCGAGTCGA
66 TGTGCGAACCCAACATATATTTTCTATAAATTATTTACATTAAGGGTGCGACCTTACCGAGTCGA
*
2726717 TTTTGGACAGCGGAAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TCTTGGACAGCGG-AAAAGGTAAGTGTGCGAACTTGAAATGCATG
*
2726762 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
*
2726827 TGTGCGAACCCAACATATATTTTCTATAAATTATTTACATTAAGGGTGCGACCTTATCGAGTCGA
66 TGTGCGAACCCAACATATATTTTCTATAAATTATTTACATTAAGGGTGCGACCTTACCGAGTCGA
2726892 TCTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TCTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
2726936 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
2726950 CGGTTGATTA
Statistics
Matches: 183, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
174 44 0.24
175 139 0.76
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
TGTGCGAACCCAACATATATTTTCTATAAATTATTTACATTAAGGGTGCGACCTTACCGAGTCGA
TCTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:2732440 original size:23 final size:24
Alignment explanation
Indices: 2732400--2732445 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
2732390 ACTTGTGACC
*
2732400 AAAAAAATATTTAAGTACCAATAT
1 AAAAAAATAATTAAGTACCAATAT
*
2732424 AAAAAAA-AATTAGGTACCAATA
1 AAAAAAATAATTAAGTACCAATA
2732446 GACTGGTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.61, C:0.09, G:0.07, T:0.24
Consensus pattern (24 bp):
AAAAAAATAATTAAGTACCAATAT
Found at i:2732673 original size:20 final size:20
Alignment explanation
Indices: 2732628--2732674 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
2732618 TTTCTTTAAA
* *
2732628 CTTTTCTTATAATTTTTATAT
1 CTTTT-TTAGAATTTTTATAC
*
2732649 ATTTTTTAGAATTTTTATAC
1 CTTTTTTAGAATTTTTATAC
2732669 CTTTTT
1 CTTTTT
2732675 ATATTCCAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (20 bp):
CTTTTTTAGAATTTTTATAC
Found at i:2734294 original size:62 final size:62
Alignment explanation
Indices: 2734195--2734339 Score: 175
Period size: 62 Copynumber: 2.3 Consensus size: 62
2734185 TGGACCCTTC
* * * * * * * *
2734195 AAAATTTTAGGAAATTATGATTTTTCACTTGAAATTTTTAGAAAATTTTAATTAGGCCCCC-
1 AAAATTTTTGGAAATTTTCATTTCTCACTTGAAATTTTAAAAAAAATTTAATTAGACCCCCT
*
2734256 AATAATTTTTGGAAATTTTCATTTCTCCCTTGAAATTTTAAAAAAAATTTAATTAGACCCCCT
1 AA-AATTTTTGGAAATTTTCATTTCTCACTTGAAATTTTAAAAAAAATTTAATTAGACCCCCT
* *
2734319 CAAATTTTTGAAAATTTTCAT
1 AAAATTTTTGGAAATTTTCAT
2734340 AATAACTTCT
Statistics
Matches: 71, Mismatches: 11, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
61 2 0.03
62 68 0.96
63 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (62 bp):
AAAATTTTTGGAAATTTTCATTTCTCACTTGAAATTTTAAAAAAAATTTAATTAGACCCCCT
Found at i:2739220 original size:38 final size:38
Alignment explanation
Indices: 2739177--2739253 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
2739167 CTAGGAAAAG
2739177 AGTGTAAATTAGTGGTCCCTAAGATAATTAAATGTTTT
1 AGTGTAAATTAGTGGTCCCTAAGATAATTAAATGTTTT
2739215 AGTGTAAATTAGTGGTCCCTAAGATAATTAAATGTTTT
1 AGTGTAAATTAGTGGTCCCTAAGATAATTAAATGTTTT
2739253 A
1 A
2739254 CTTCCAAGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (38 bp):
AGTGTAAATTAGTGGTCCCTAAGATAATTAAATGTTTT
Found at i:2740925 original size:21 final size:21
Alignment explanation
Indices: 2740899--2740943 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
2740889 TATATAGTTG
2740899 TACATATTTCTAAGAAATACA
1 TACATATTTCTAAGAAATACA
2740920 TACATATTTCTAAGAAATACA
1 TACATATTTCTAAGAAATACA
2740941 TAC
1 TAC
2740944 TTTTGAGTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (21 bp):
TACATATTTCTAAGAAATACA
Found at i:2746091 original size:17 final size:17
Alignment explanation
Indices: 2746069--2746110 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
2746059 TATTTAGTAA
*
2746069 TATTTTTATCTTAAAAG
1 TATTTTTATCCTAAAAG
*
2746086 TATTTTTTGTCCTAAAAG
1 TA-TTTTTATCCTAAAAG
2746104 TATTTTT
1 TATTTTT
2746111 TAAAAGTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (17 bp):
TATTTTTATCCTAAAAG
Found at i:2747848 original size:26 final size:28
Alignment explanation
Indices: 2747803--2747857 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
2747793 TGAGTTATTA
*
2747803 AATTTCTTTCTGAGTATTCTTTT-GAAG
1 AATTTCTCTCTGAGTATTCTTTTAGAAG
*
2747830 AATTTCTCT-TGAGTTTTCTTTTAGAAG
1 AATTTCTCTCTGAGTATTCTTTTAGAAG
2747857 A
1 A
2747858 GTTTTAACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 12 0.48
27 13 0.52
ACGTcount: A:0.24, C:0.11, G:0.15, T:0.51
Consensus pattern (28 bp):
AATTTCTCTCTGAGTATTCTTTTAGAAG
Found at i:2749842 original size:18 final size:17
Alignment explanation
Indices: 2749809--2749848 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
2749799 GAAAATAATA
*
2749809 ATTTTCTTTTTATTATT
1 ATTTTATTTTTATTATT
2749826 ATTTTATTTTCTATTATT
1 ATTTTATTTT-TATTATT
*
2749844 GTTTT
1 ATTTT
2749849 CAAAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.75
Consensus pattern (17 bp):
ATTTTATTTTTATTATT
Found at i:2759155 original size:13 final size:12
Alignment explanation
Indices: 2759139--2759183 Score: 63
Period size: 13 Copynumber: 3.6 Consensus size: 12
2759129 ACGGTATTGT
2759139 AAAAAAAATATAA
1 AAAAAAAAT-TAA
*
2759152 AAAAAAATTTGAA
1 AAAAAAAATT-AA
2759165 AAAAAAAATTAA
1 AAAAAAAATTAA
2759177 AAAAAAA
1 AAAAAAA
2759184 GTTTGTATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 10 0.34
13 19 0.66
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (12 bp):
AAAAAAAATTAA
Found at i:2759156 original size:12 final size:12
Alignment explanation
Indices: 2759139--2759183 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
2759129 ACGGTATTGT
2759139 AAAAAAAATATA
1 AAAAAAAATATA
*
2759151 AAAAAAAATTTGA
1 AAAAAAAATAT-A
2759164 AAAAAAAA-ATTA
1 AAAAAAAATA-TA
2759176 AAAAAAAA
1 AAAAAAAA
2759184 GTTTGTATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 19 0.66
13 10 0.34
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (12 bp):
AAAAAAAATATA
Found at i:2759173 original size:26 final size:26
Alignment explanation
Indices: 2759139--2759188 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
2759129 ACGGTATTGT
2759139 AAAAAAAATATAAAAAAAAA-TTTGAA
1 AAAAAAAAT-TAAAAAAAAAGTTTGAA
2759165 AAAAAAAATTAAAAAAAAAGTTTG
1 AAAAAAAATTAAAAAAAAAGTTTG
2759189 TATTCAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (26 bp):
AAAAAAAATTAAAAAAAAAGTTTGAA
Found at i:2759262 original size:30 final size:29
Alignment explanation
Indices: 2759226--2759295 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 29
2759216 TTAGTATTGA
**
2759226 AGAAAAAAAAAGAAAAAAAAATTCGGAATT
1 AGAAAAAAAAAGAAAAAAAAA-TCAAAATT
*
2759256 AGAAAAAAGGAAGAAAAAAAAATCAAAATT
1 AGAAAAAA-AAAGAAAAAAAAATCAAAATT
2759286 -GAAAAAAAAA
1 AGAAAAAAAAA
2759296 AAAGAGTGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
28 2 0.06
29 7 0.20
30 14 0.40
31 12 0.34
ACGTcount: A:0.74, C:0.03, G:0.13, T:0.10
Consensus pattern (29 bp):
AGAAAAAAAAAGAAAAAAAAATCAAAATT
Found at i:2759283 original size:21 final size:21
Alignment explanation
Indices: 2759259--2759298 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2759249 CGGAATTAGA
*
2759259 AAAAAGGAAGAAAAAAAAATC
1 AAAAAGGAAAAAAAAAAAATC
**
2759280 AAAATTGAAAAAAAAAAAA
1 AAAAAGGAAAAAAAAAAAA
2759299 GAGTGATTGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.80, C:0.03, G:0.10, T:0.07
Consensus pattern (21 bp):
AAAAAGGAAAAAAAAAAAATC
Found at i:2760226 original size:21 final size:21
Alignment explanation
Indices: 2760186--2760244 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
2760176 AATCTTGAAT
*
2760186 GAAATTGAGAGAAGAA-AAAAA
1 GAAA-TGAGAGAAAAAGAAAAA
2760207 GAAATGAGAGAAAAAGAAAAA
1 GAAATGAGAGAAAAAGAAAAA
* *
2760228 GAAATAAAAGAAAAAGA
1 GAAATGAGAGAAAAAGA
2760245 TGAAAATGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 10 0.29
21 24 0.71
ACGTcount: A:0.71, C:0.00, G:0.22, T:0.07
Consensus pattern (21 bp):
GAAATGAGAGAAAAAGAAAAA
Found at i:2760236 original size:15 final size:14
Alignment explanation
Indices: 2760197--2760244 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
2760187 AAATTGAGAG
2760197 AAGAAAAAAAGAAA
1 AAGAAAAAAAGAAA
* *
2760211 TGAGAGAAAAAGAAA
1 -AAGAAAAAAAGAAA
2760226 AAGAAATAAAAGAAA
1 AAGAAA-AAAAGAAA
2760241 AAGA
1 AAGA
2760245 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (14 bp):
AAGAAAAAAAGAAA
Found at i:2772449 original size:19 final size:18
Alignment explanation
Indices: 2772406--2772449 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
2772396 TTAATAATCT
* *
2772406 TGAATGTATATGATGACA
1 TGAATGTAGATGATGAAA
2772424 TGTAATGTAGATGCATGAAA
1 TG-AATGTAGATG-ATGAAA
2772444 TGAATG
1 TGAATG
2772450 CAAAAAGGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 13 0.59
20 7 0.32
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.32
Consensus pattern (18 bp):
TGAATGTAGATGATGAAA
Found at i:2774765 original size:31 final size:32
Alignment explanation
Indices: 2774729--2774793 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
2774719 CTTAGATAAT
2774729 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
2774760 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
2774792 TT
1 TT
2774794 GTAATTTTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 9 0.27
32 24 0.73
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (32 bp):
TTTAAAGAGTTTTTATTAGGATTCAATTACTC
Found at i:2775366 original size:20 final size:19
Alignment explanation
Indices: 2775333--2775379 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
2775323 CTTATTCTTT
2775333 AAAAAAAAGAAAAAAGCGC
1 AAAAAAAAGAAAAAAGCGC
*
2775352 AAAAAAGAAGCAAAAAGCGC
1 AAAAAA-AAGAAAAAAGCGC
2775372 AAAAAAAA
1 AAAAAAAA
2775380 AGTTGCCTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.74, C:0.11, G:0.15, T:0.00
Consensus pattern (19 bp):
AAAAAAAAGAAAAAAGCGC
Done.