Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014628.1 Kokia drynarioides strain JFW-HI SEQ_129667, whole genome shotgun sequence
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: 761112
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 101 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:271371 original size:21 final size:24
Alignment explanation
Indices: 271345--271394 Score: 70
Period size: 21 Copynumber: 2.2 Consensus size: 24
271335 AAATCAATAC
*
271345 AGAGAGTATTCA-A-AGTGG-AAT
1 AGAGAGTATACAGACAGTGGTAAT
271366 AGAGAGTATACAGACAGTGGTAAT
1 AGAGAGTATACAGACAGTGGTAAT
271390 AGAGA
1 AGAGA
271395 AGCATAAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 11 0.44
22 1 0.04
23 5 0.20
24 8 0.32
ACGTcount: A:0.44, C:0.06, G:0.30, T:0.20
Consensus pattern (24 bp):
AGAGAGTATACAGACAGTGGTAAT
Found at i:271622 original size:16 final size:16
Alignment explanation
Indices: 271601--271634 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
271591 GTATATTTAA
271601 TAAATAAT-TATAATAT
1 TAAATAATAT-TAATAT
271617 TAAATAATATTAATAT
1 TAAATAATATTAATAT
271633 TA
1 TA
271635 GTAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 16 0.94
17 1 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAATAATATTAATAT
Found at i:272859 original size:29 final size:30
Alignment explanation
Indices: 272821--273125 Score: 232
Period size: 29 Copynumber: 10.4 Consensus size: 30
272811 TCAACATAGT
* * *
272821 ATTTTGACCCTCGAACTTC-CAAAAATTAC
1 ATTTTAACCCTCAAACTTCTCCAAAATTAC
*
272850 ATTTTGACCCT-AAACTT-TCCTAAAATTAC
1 ATTTTAACCCTCAAACTTCTCC-AAAATTAC
* * * *
272879 CTTTTAACCCTTAAACTT-TTCAAAATTAT
1 ATTTTAACCCTCAAACTTCTCCAAAATTAC
* * * * *
272908 GTTTTGACCCCCAAACTTC-CTAAAATCAC
1 ATTTTAACCCTCAAACTTCTCCAAAATTAC
* * *
272937 ATTTTAACCCTAAAATTTCTCCAAAATCAC
1 ATTTTAACCCTCAAACTTCTCCAAAATTAC
* * *
272967 ATTTTAATCCT-AAATTTTCTCCAAAATTCC
1 ATTTTAACCCTCAAA-CTTCTCCAAAATTAC
* * *
272997 ATTTTGA-CCTCGAACTTCTCCAAAATTCC
1 ATTTTAACCCTCAAACTTCTCCAAAATTAC
* **
273026 ATTTTTACCCAAAAACTTCTCCAAAATTAC
1 ATTTTAACCCTCAAACTTCTCCAAAATTAC
* * * *
273056 ATTTTAACCCCTAAAATTTCT-AAAAATCAC
1 ATTTTAA-CCCTCAAACTTCTCCAAAATTAC
* *
273086 ATTTTAACCCT-AAACTTTTCTAAAATTAC
1 ATTTTAACCCTCAAACTTCTCCAAAATTAC
*
273115 CTTTTAACCCT
1 ATTTTAACCCT
273126 AAATTCCTCG
Statistics
Matches: 225, Mismatches: 41, Indels: 20
0.79 0.14 0.07
Matches are distributed among these distances:
28 12 0.05
29 116 0.52
30 86 0.38
31 11 0.05
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.36
Consensus pattern (30 bp):
ATTTTAACCCTCAAACTTCTCCAAAATTAC
Found at i:272896 original size:30 final size:29
Alignment explanation
Indices: 272837--273128 Score: 227
Period size: 30 Copynumber: 9.9 Consensus size: 29
272827 ACCCTCGAAC
* *
272837 TTCCAAAAATTACATTTTGACCCTAAACT
1 TTCCTAAAATTACATTTTAACCCTAAACT
*
272866 TTCCTAAAATTACCTTTTAACCCTTAAACT
1 TTCCTAAAATTACATTTTAACCC-TAAACT
* ** * *
272896 TTTC-AAAATTATGTTTTGACCCCCAAAC-
1 TTCCTAAAATTACATTTT-AACCCTAAACT
* *
272924 TTCCTAAAATCACATTTTAACCCTAAAAT
1 TTCCTAAAATTACATTTTAACCCTAAACT
* * * *
272953 TTCTCCAAAATCACATTTTAATCCTAAATT
1 TTC-CTAAAATTACATTTTAACCCTAAACT
* * * *
272983 TTCTCCAAAATTCCATTTTGA-CCTCGAACT
1 TTC-CTAAAATTACATTTTAACCCT-AAACT
* * *
273013 TCTCC-AAAATTCCATTTTTACCCAAAAACT
1 T-TCCTAAAATTACATTTTAACCC-TAAACT
*
273043 TCTCC-AAAATTACATTTTAACCCCTAAAAT
1 T-TCCTAAAATTACATTTTAA-CCCTAAACT
*
273073 TT-CTAAAAATCACATTTTAACCCTAAACT
1 TTCCT-AAAATTACATTTTAACCCTAAACT
* *
273102 TTTCTAAAATTACCTTTTAACCCTAAA
1 TTCCTAAAATTACATTTTAACCCTAAA
273129 TTCCTCGAAA
Statistics
Matches: 216, Mismatches: 34, Indels: 26
0.78 0.12 0.09
Matches are distributed among these distances:
28 11 0.05
29 96 0.44
30 104 0.48
31 5 0.02
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.36
Consensus pattern (29 bp):
TTCCTAAAATTACATTTTAACCCTAAACT
Found at i:273016 original size:59 final size:60
Alignment explanation
Indices: 272842--273128 Score: 200
Period size: 59 Copynumber: 4.9 Consensus size: 60
272832 CGAACTTCCA
* * * * * * * *
272842 AAAATTACATTTTGACCCTAAACTTTC-CTAAAATTACCTTTTAACCCTTAAACTT-TTC
1 AAAATCACATTTTAACCCTAAATTTTCTCCAAAATTACATTTTAACCCCTAAAATTCTCC
* ** * * * * *
272900 AAAATTATGTTTTGACCCCCAAA-CTTC-CTAAAATCACATTTTAA-CCCTAAAATTTCTCC
1 AAAATCACATTTT-AACCCTAAATTTTCTCCAAAATTACATTTTAACCCCTAAAA-TTCTCC
* * * * * *
272959 AAAATCACATTTTAATCCTAAATTTTCTCCAAAATTCCATTTTGACCTC-GAACTTCTCC
1 AAAATCACATTTTAACCCTAAATTTTCTCCAAAATTACATTTTAACCCCTAAAATTCTCC
* * ** *
273018 AAAATTC-CATTTTTACCCAAAAACTTCTCCAAAATTACATTTTAACCCCTAAAATT-TCTA
1 AAAA-TCACATTTTAACCCTAAATTTTCTCCAAAATTACATTTTAACCCCTAAAATTCTC-C
*
273078 AAAATCACATTTTAACCCTAAACTTTTCT--AAAATTACCTTTTAA-CCCTAAA
1 AAAATCACATTTTAACCCTAAA-TTTTCTCCAAAATTACATTTTAACCCCTAAA
273129 TTCCTCGAAA
Statistics
Matches: 177, Mismatches: 41, Indels: 22
0.74 0.17 0.09
Matches are distributed among these distances:
57 6 0.03
58 44 0.25
59 83 0.47
60 38 0.21
61 6 0.03
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.36
Consensus pattern (60 bp):
AAAATCACATTTTAACCCTAAATTTTCTCCAAAATTACATTTTAACCCCTAAAATTCTCC
Found at i:279072 original size:4 final size:4
Alignment explanation
Indices: 279022--279079 Score: 53
Period size: 4 Copynumber: 14.5 Consensus size: 4
279012 TAAATAAACA
* * * * * * *
279022 AATG AACG AATG AGTG AATG GATG GATG AATT AATG AACG AACG AATG
1 AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG
279070 AATG AATG AA
1 AATG AATG AA
279080 ATTGGGGCAC
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.47, C:0.05, G:0.28, T:0.21
Consensus pattern (4 bp):
AATG
Found at i:282783 original size:237 final size:237
Alignment explanation
Indices: 282368--282838 Score: 843
Period size: 237 Copynumber: 2.0 Consensus size: 237
282358 AAAATGTATT
*
282368 CGATTTACTTGTAACTTGACTAAGATGTGTTCACCAAACTTATCTAATCTAAAACTTAAATTAGA
1 CGATTTACTTGTAACTTGACTAAGACGTGTTCACCAAACTTATCTAATCTAAAACTTAAATTAGA
* * * * * *
282433 GATTTTTACTTTTAACAAGAACCCTAAAGGATACCTAAATAATTCTAGTATACTACCTTCCATTC
66 GATTTTTACTTCTAACAAGAACCCTAAAGGATAACTAAATAATTCTAGTAAAATACCTTCAATTA
282498 TTAAAATTAATTCTATTTTAGAATCCTAAAAAAACCTAAAAATTACTAATGAATTAAGAGAAATA
131 TTAAAATTAATTCTATTTTAGAATCCTAAAAAAACCTAAAAATTACTAATGAATTAAGAGAAATA
282563 TTAAAATTCATCTACAACTTATTCGATCTTTTATCATTACTC
196 TTAAAATTCATCTACAACTTATTCGATCTTTTATCATTACTC
*
282605 CGATTTACTTGTAACTTGACTAAGACGTGTTCACCAAACTTATCTAATTTAAAACTTAAATTAGA
1 CGATTTACTTGTAACTTGACTAAGACGTGTTCACCAAACTTATCTAATCTAAAACTTAAATTAGA
* * *
282670 GATTTTTACTTCTAACGAGAACCCTAAATGATAATTAAATAATTCTAGTAAAATACCTTCAATTA
66 GATTTTTACTTCTAACAAGAACCCTAAAGGATAACTAAATAATTCTAGTAAAATACCTTCAATTA
282735 TTAAAATTAATTCTATTTTAGAATCCTAAAAAAACCTAAAAATTACTAATGAATTAAGAGAAATA
131 TTAAAATTAATTCTATTTTAGAATCCTAAAAAAACCTAAAAATTACTAATGAATTAAGAGAAATA
282800 TTAAAATTCATCTACAACTTATTCGATCTTTTATCATTA
196 TTAAAATTCATCTACAACTTATTCGATCTTTTATCATTA
282839 TTATTATTTT
Statistics
Matches: 223, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
237 223 1.00
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (237 bp):
CGATTTACTTGTAACTTGACTAAGACGTGTTCACCAAACTTATCTAATCTAAAACTTAAATTAGA
GATTTTTACTTCTAACAAGAACCCTAAAGGATAACTAAATAATTCTAGTAAAATACCTTCAATTA
TTAAAATTAATTCTATTTTAGAATCCTAAAAAAACCTAAAAATTACTAATGAATTAAGAGAAATA
TTAAAATTCATCTACAACTTATTCGATCTTTTATCATTACTC
Found at i:284284 original size:56 final size:55
Alignment explanation
Indices: 284220--284435 Score: 256
Period size: 56 Copynumber: 3.9 Consensus size: 55
284210 TAAAACATCG
* * * *
284220 ATAAAGAAAACCTTCGTGGTAGACTTTGGAAAGGTAAGCCTTTGTGGCAAACCTCT
1 ATAAAGAAAGCCTTTGTGATAAACTTTGGAAAGGTAAGCCTTTGTGG-AAACCTCT
** * *
284276 ATAAAGAAAGCCTTTGTGGCAAACTATT-GAAAGGTAAGCCCTTGTCAGGTGAACCTCT
1 ATAAAGAAAGCCTTTGTGATAAACT-TTGGAAAGGTAAGCCTTTGT--GG-AAACCTCT
*
284334 ATAAAGAAAGCCTTTGTGAAAAACTTTGGAAAGGTAAGCCTTTGTGGAGAACCTCT
1 ATAAAGAAAGCCTTTGTGATAAACTTTGGAAAGGTAAGCCTTTGTGGA-AACCTCT
** *
284390 ATAAAGAAAGCCTTTGTGATAAACCCTAGAAAGGT-AGCCTTTGTGG
1 ATAAAGAAAGCCTTTGTGATAAACTTTGGAAAGGTAAGCCTTTGTGG
284436 TGAACCTAAG
Statistics
Matches: 140, Mismatches: 15, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
55 11 0.08
56 77 0.55
57 4 0.03
58 48 0.34
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (55 bp):
ATAAAGAAAGCCTTTGTGATAAACTTTGGAAAGGTAAGCCTTTGTGGAAACCTCT
Found at i:284441 original size:27 final size:28
Alignment explanation
Indices: 284248--284442 Score: 108
Period size: 28 Copynumber: 6.9 Consensus size: 28
284238 GTAGACTTTG
**
284248 GAAAGGTAAGCCTTTGTGGCAAACCTCTA
1 GAAAGGT-AGCCTTTGTGGTGAACCTCTA
* ** * * * *
284277 TAAAGAAAGCCTTTGTGG-CAAACTATT
1 GAAAGGTAGCCTTTGTGGTGAACCTCTA
*
284304 GAAAGGTAAGCCCTTGTCAGGTGAACCTCTA
1 GAAAGGT-AGCCTTTGT--GGTGAACCTCTA
* ** ** * * *
284335 TAAAGAAAGCCTTTGT-GAAAAACTTTG
1 GAAAGGTAGCCTTTGTGGTGAACCTCTA
*
284362 GAAAGGTAAGCCTTTGTGGAGAACCTCTA
1 GAAAGGT-AGCCTTTGTGGTGAACCTCTA
* ** * *
284391 TAAAGAAAGCCTTTGTGATAAACC-CTA
1 GAAAGGTAGCCTTTGTGGTGAACCTCTA
284418 GAAAGGTAGCCTTTGTGGTGAACCT
1 GAAAGGTAGCCTTTGTGGTGAACCT
284443 AAGCATTCGT
Statistics
Matches: 117, Mismatches: 42, Indels: 15
0.67 0.24 0.09
Matches are distributed among these distances:
27 41 0.35
28 42 0.36
29 15 0.13
30 10 0.09
31 9 0.08
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.26
Consensus pattern (28 bp):
GAAAGGTAGCCTTTGTGGTGAACCTCTA
Found at i:284495 original size:28 final size:28
Alignment explanation
Indices: 284459--284562 Score: 129
Period size: 28 Copynumber: 3.7 Consensus size: 28
284449 TCGTGGCAAA
* * *
284459 CTCTATTAAAGGAAGAT-TTTATGGCGAT
1 CTCTGTTAAAGGAAG-TCTTTGTGGCGCT
* *
284487 CTCTGTTAAATGAAGTCTTTGTAGCGCT
1 CTCTGTTAAAGGAAGTCTTTGTGGCGCT
*
284515 CTCTGTTAAAGGAAGTCTTTGTGGTGCT
1 CTCTGTTAAAGGAAGTCTTTGTGGCGCT
*
284543 CTCTGTTAAAGGAGGTCTTT
1 CTCTGTTAAAGGAAGTCTTT
284563 ATGGTTATCG
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
27 1 0.02
28 65 0.98
ACGTcount: A:0.23, C:0.14, G:0.24, T:0.38
Consensus pattern (28 bp):
CTCTGTTAAAGGAAGTCTTTGTGGCGCT
Found at i:285675 original size:117 final size:117
Alignment explanation
Indices: 285469--285705 Score: 474
Period size: 117 Copynumber: 2.0 Consensus size: 117
285459 GTGGTAACAC
285469 CTAATATTCAGATGAGATGAATTGGATCGGGTTTAGAGTGTTATAGTAACCTTAACAGTCTTGGG
1 CTAATATTCAGATGAGATGAATTGGATCGGGTTTAGAGTGTTATAGTAACCTTAACAGTCTTGGG
285534 GCGACCTTTAGAAGACTCAACAATTTACTTAACCTCTTCACCATCAGCAAGG
66 GCGACCTTTAGAAGACTCAACAATTTACTTAACCTCTTCACCATCAGCAAGG
285586 CTAATATTCAGATGAGATGAATTGGATCGGGTTTAGAGTGTTATAGTAACCTTAACAGTCTTGGG
1 CTAATATTCAGATGAGATGAATTGGATCGGGTTTAGAGTGTTATAGTAACCTTAACAGTCTTGGG
285651 GCGACCTTTAGAAGACTCAACAATTTACTTAACCTCTTCACCATCAGCAAGG
66 GCGACCTTTAGAAGACTCAACAATTTACTTAACCTCTTCACCATCAGCAAGG
285703 CTA
1 CTA
285706 TGAAAACCCT
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
117 120 1.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (117 bp):
CTAATATTCAGATGAGATGAATTGGATCGGGTTTAGAGTGTTATAGTAACCTTAACAGTCTTGGG
GCGACCTTTAGAAGACTCAACAATTTACTTAACCTCTTCACCATCAGCAAGG
Found at i:287176 original size:27 final size:27
Alignment explanation
Indices: 287144--287229 Score: 172
Period size: 27 Copynumber: 3.2 Consensus size: 27
287134 GTGTACATCT
287144 TTGTTCTTTTGTTTAAAATGAACATGA
1 TTGTTCTTTTGTTTAAAATGAACATGA
287171 TTGTTCTTTTGTTTAAAATGAACATGA
1 TTGTTCTTTTGTTTAAAATGAACATGA
287198 TTGTTCTTTTGTTTAAAATGAACATGA
1 TTGTTCTTTTGTTTAAAATGAACATGA
287225 TTGTT
1 TTGTT
287230 TTGATACAAG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.28, C:0.07, G:0.15, T:0.50
Consensus pattern (27 bp):
TTGTTCTTTTGTTTAAAATGAACATGA
Found at i:287623 original size:33 final size:34
Alignment explanation
Indices: 287552--287630 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 34
287542 TTATTGAAAG
*
287552 TGTTGAAGACACCAACGAAGTAATAAGAGTACTG
1 TGTTGAAGACACCAACGAAGTAATAAGAGTACTC
* *
287586 TGTTGAAGACACCAATGAAGT-ATTAGAGTACTC
1 TGTTGAAGACACCAACGAAGTAATAAGAGTACTC
287619 TGTTGAAGACAC
1 TGTTGAAGACAC
287631 TTTCAACTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 22 0.52
34 20 0.48
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.24
Consensus pattern (34 bp):
TGTTGAAGACACCAACGAAGTAATAAGAGTACTC
Found at i:293859 original size:6 final size:6
Alignment explanation
Indices: 293836--293869 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
293826 TCGCCCTCAC
*
293836 AATAAA AATACA AA-AAA AATAAA AATAAA AATAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAA
293870 TTTTCAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (6 bp):
AATAAA
Found at i:293884 original size:20 final size:19
Alignment explanation
Indices: 293855--293916 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
293845 ACAAAAAAAA
293855 TAAAAA-TAAAAATAATTT
1 TAAAAATTAAAAATAATTT
293873 TCAAAAATTAAAAATAATTT
1 T-AAAAATTAAAAATAATTT
* *
293893 TTAAAATTGAAAAT-ATTT
1 TAAAAATTAAAAATAATTT
293911 ATAAAA
1 -TAAAA
293917 TTTATATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
18 5 0.13
19 20 0.53
20 13 0.34
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (19 bp):
TAAAAATTAAAAATAATTT
Found at i:293915 original size:18 final size:19
Alignment explanation
Indices: 293854--293918 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 19
293844 TACAAAAAAA
*
293854 ATAAAAATAAAAATAATTT
1 ATAAAATTAAAAATAATTT
293873 -TCAAAAATTAAAAATAATTT
1 AT--AAAATTAAAAATAATTT
* *
293893 TTAAAATTGAAAAT-ATTT
1 ATAAAATTAAAAATAATTT
293911 ATAAAATT
1 ATAAAATT
293919 TATATTTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
18 12 0.30
19 11 0.28
20 16 0.40
21 1 0.03
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (19 bp):
ATAAAATTAAAAATAATTT
Found at i:294971 original size:99 final size:97
Alignment explanation
Indices: 294800--294991 Score: 303
Period size: 99 Copynumber: 2.0 Consensus size: 97
294790 TTGAAAAAGG
* *
294800 GTATTTGATTATCCCAATTTAAAAAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCAAAAT
1 GTATTCGATTATCCCAATTTAAAAAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCAAAAC
* *
294865 CCTAGATAAAGGAATATTGCCTTGATTTAAGA
66 CCGAGATAAAAGAATATTGCCTTGATTTAAGA
** *
294897 GTATTCGATTATCCCGGTTTGAAGAAAAAAATTGCGCCTAGTAAGTTAAGGCACAAATTTTCAAA
1 GTATTCGATTATCCCAATTT-AA-AAAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCAAA
294962 ACCCGAGATAAAAGAATATTGCCTTGATTT
64 ACCCGAGATAAAAGAATATTGCCTTGATTT
294992 TTAAATATTG
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
97 17 0.20
98 2 0.02
99 67 0.78
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (97 bp):
GTATTCGATTATCCCAATTTAAAAAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCAAAAC
CCGAGATAAAAGAATATTGCCTTGATTTAAGA
Found at i:295312 original size:30 final size:30
Alignment explanation
Indices: 295258--295584 Score: 177
Period size: 29 Copynumber: 11.2 Consensus size: 30
295248 AGTTTCGAAG
* *
295258 AGTTTG-GGGTTAAAATGCAA-TTTTGGAA
1 AGTTTGAGGGGTAAAATGTAATTTTTGGAA
* *
295286 AGTTTTAGGGGTAAAATGTCATTTTTGG-A
1 AGTTTGAGGGGTAAAATGTAATTTTTGGAA
* * *
295315 AGATCG-GGGGTAAAAATGTAATTTTTAG-A
1 AGTTTGAGGGGT-AAAATGTAATTTTTGGAA
* * *
295344 AGTTCGA-GGGTAAAAATGTGATCTTT-GAA
1 AGTTTGAGGGGT-AAAATGTAATTTTTGGAA
* ** *
295373 AGTTCGAGGGCAAAAATGTGATTTTTGG-A
1 AGTTTGAGGGGTAAAATGTAATTTTTGGAA
* * *
295402 AGTTCGAAGGGTAAAACTGTGATTTTTGG-A
1 AGTTTGAGGGGTAAAA-TGTAATTTTTGGAA
* * * **
295432 CGTTCG-GAGCAAAAATGTAATTTTTGG-A
1 AGTTTGAGGGGTAAAATGTAATTTTTGGAA
* * *
295460 AGTTCGA-GAGCAAAAGTGTAATTTTT-GAGA
1 AGTTTGAGGGGTAAAA-TGTAATTTTTGGA-A
*
295490 AGTTTGA-GGGTCAAAATGCAA-TTTTGGAAA
1 AGTTTGAGGGGT-AAAATGTAATTTTTGG-AA
*
295520 AGTTT-AGGGGTTAAAATATAA-TTTTGGAAA
1 AGTTTGAGGGG-TAAAATGTAATTTTTGG-AA
* *
295550 AATTT-AGAGGTCAAAATGTAATTTTTGGAA
1 AGTTTGAGGGGT-AAAATGTAATTTTTGGAA
295580 AGTTT
1 AGTTT
295585 AAGGACCTTT
Statistics
Matches: 241, Mismatches: 39, Indels: 36
0.76 0.12 0.11
Matches are distributed among these distances:
28 33 0.14
29 108 0.45
30 88 0.37
31 12 0.05
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.34
Consensus pattern (30 bp):
AGTTTGAGGGGTAAAATGTAATTTTTGGAA
Found at i:295330 original size:29 final size:29
Alignment explanation
Indices: 295294--295507 Score: 225
Period size: 29 Copynumber: 7.4 Consensus size: 29
295284 AAAGTTTTAG
* * *
295294 GGGT-AAAATGTCATTTTTGGAAGATCGG
1 GGGTAAAAATGTGATTTTTGGAAGTTCGA
* *
295322 GGGTAAAAATGTAATTTTTAGAAGTTCGA
1 GGGTAAAAATGTGATTTTTGGAAGTTCGA
* *
295351 GGGTAAAAATGTGATCTTTGAAAGTTCGA
1 GGGTAAAAATGTGATTTTTGGAAGTTCGA
*
295380 GGGCAAAAATGTGATTTTTGGAAGTTCGAA
1 GGGTAAAAATGTGATTTTTGGAAGTTCG-A
* *
295410 GGGTAAAACTGTGATTTTTGGACGTTCG-
1 GGGTAAAAATGTGATTTTTGGAAGTTCGA
* * *
295438 GAGCAAAAATGTAATTTTTGGAAGTTCGA
1 GGGTAAAAATGTGATTTTTGGAAGTTCGA
* * * * *
295467 GAGCAAAAGTGTAATTTTTGAGAAGTTTGA
1 GGGTAAAAATGTGATTTTTG-GAAGTTCGA
*
295497 GGGTCAAAATG
1 GGGTAAAAATG
295508 CAATTTTGGA
Statistics
Matches: 157, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
28 27 0.17
29 89 0.57
30 41 0.26
ACGTcount: A:0.33, C:0.07, G:0.29, T:0.32
Consensus pattern (29 bp):
GGGTAAAAATGTGATTTTTGGAAGTTCGA
Found at i:295338 original size:58 final size:57
Alignment explanation
Indices: 295263--295519 Score: 207
Period size: 58 Copynumber: 4.4 Consensus size: 57
295253 CGAAGAGTTT
* * ** * *
295263 GGGGTTAAAATGCAATTTTGGAAAGTTTTAGGGGTAAAATGTCATTTTTGGAAGATCG
1 GGGGTAAAAATGTAATTTTGGAAAGTTCGA-GGGTAAAATGTGATTTTTGGAAGTTCG
* * *
295321 GGGGTAAAAATGTAATTTT-TAGAAGTTCGAGGGTAAAAATGTGATCTTTGAAAGTTCG
1 GGGGTAAAAATGTAATTTTGGA-AAGTTCGAGGGT-AAAATGTGATTTTTGGAAGTTCG
* * * *
295379 AGGGCAAAAATGTGATTTTTGG-AAGTTCGAAGGGTAAAACTGTGATTTTTGGACGTTC-
1 GGGGTAAAAATGT-AATTTTGGAAAGTTCG-AGGGTAAAA-TGTGATTTTTGGAAGTTCG
* * * * * *
295437 GGAGCAAAAATGTAATTTTTGG-AAGTTCGAGAGCAAAAGTGTAATTTTTGAGAAGTTTG
1 GGGGTAAAAATGTAA-TTTTGGAAAGTTCGAGGGTAAAA-TGTGATTTTTG-GAAGTTCG
* * *
295496 AGGGTCAAAATGCAATTTTGGAAA
1 GGGGTAAAAATGTAATTTTGGAAA
295520 AGTTTAGGGG
Statistics
Matches: 159, Mismatches: 30, Indels: 19
0.76 0.14 0.09
Matches are distributed among these distances:
57 23 0.14
58 99 0.62
59 37 0.23
ACGTcount: A:0.33, C:0.06, G:0.28, T:0.32
Consensus pattern (57 bp):
GGGGTAAAAATGTAATTTTGGAAAGTTCGAGGGTAAAATGTGATTTTTGGAAGTTCG
Found at i:295579 original size:31 final size:30
Alignment explanation
Indices: 295470--295585 Score: 128
Period size: 30 Copynumber: 3.8 Consensus size: 30
295460 AGTTCGAGAG
* *
295470 CAAAAGTGTAATTTTTGAGAAGTTT-GAGGGT
1 CAAAA-TGTAATTTTGGAAAAGTTTAGA-GGT
* *
295501 CAAAATGCAATTTTGGAAAAGTTTAGGGGT
1 CAAAATGTAATTTTGGAAAAGTTTAGAGGT
* * *
295531 TAAAATATAATTTTGGAAAAATTTAGAGGT
1 CAAAATGTAATTTTGGAAAAGTTTAGAGGT
295561 CAAAATGTAATTTTTGG-AAAGTTTA
1 CAAAATGTAA-TTTTGGAAAAGTTTA
295586 AGGACCTTTT
Statistics
Matches: 71, Mismatches: 12, Indels: 5
0.81 0.14 0.06
Matches are distributed among these distances:
30 59 0.83
31 12 0.17
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.35
Consensus pattern (30 bp):
CAAAATGTAATTTTGGAAAAGTTTAGAGGT
Found at i:297386 original size:12 final size:11
Alignment explanation
Indices: 297380--297481 Score: 66
Period size: 11 Copynumber: 9.0 Consensus size: 11
297370 TAATTAAACT
297380 TTAAATTTAAA
1 TTAAATTTAAA
*
297391 TTCAAA-ATAAA
1 TT-AAATTTAAA
297402 TTTAAATTTAAA
1 -TTAAATTTAAA
*
297414 ATAAATTTAAA
1 TTAAATTTAAA
* * *
297425 CTCAAA-ATAAGT
1 -TTAAATTTAA-A
297437 TTAAATTTAAA
1 TTAAATTTAAA
*
297448 ATAAATTTAAA
1 TTAAATTTAAA
*
297459 CTTAAA-ATAAA
1 -TTAAATTTAAA
297470 TTAAAATTTAAA
1 TT-AAATTTAAA
297482 ATTTAAAATT
Statistics
Matches: 68, Mismatches: 14, Indels: 17
0.69 0.14 0.17
Matches are distributed among these distances:
10 2 0.03
11 43 0.63
12 23 0.34
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:297401 original size:17 final size:17
Alignment explanation
Indices: 297381--297483 Score: 152
Period size: 17 Copynumber: 6.1 Consensus size: 17
297371 AATTAAACTT
*
297381 TAAATTTAAATTCAAAA
1 TAAATTTAAATTTAAAA
297398 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
297415 TAAATTTAAACTCAAAA
1 TAAATTTAAATTTAAAA
*
297432 TAAGTTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
297449 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
*
297466 TAAATTAAAATTTAAAA
1 TAAATTTAAATTTAAAA
297483 T
1 T
297484 TTAAAATTGT
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 76 1.00
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:297415 original size:7 final size:6
Alignment explanation
Indices: 297373--297488 Score: 80
Period size: 6 Copynumber: 19.8 Consensus size: 6
297363 GGACTTTTAA
* * *
297373 TTAAACT TTAAAT TTAAAT TCAAA- ATAAAT TTAAAT TTAAA- ATAAAT
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* * * * * *
297420 TTAAAC TCAAA- ATAAGT TTAAAT TTAAA- ATAAAT TTAAAC TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
297465 ATAAAT TAAAAT TTAAAAT TTAAA
1 TTAAAT TTAAAT TT-AAAT TTAAA
297489 ATTGTGTTCA
Statistics
Matches: 83, Mismatches: 20, Indels: 13
0.72 0.17 0.11
Matches are distributed among these distances:
5 17 0.20
6 55 0.66
7 11 0.13
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (6 bp):
TTAAAT
Found at i:297936 original size:39 final size:38
Alignment explanation
Indices: 297891--298724 Score: 388
Period size: 39 Copynumber: 21.4 Consensus size: 38
297881 TACCCTATGA
*
297891 TCGGGGTAAGAGATTGACTAATGGTGATCTGCCCCAAGC
1 TCGGGGTAAGAGATTG-CTAATGGTGATCTGCCCCAGGC
* * * * * * *
297930 TTGGGGTAAGAGA-T-CGAATGATTGCAATTTGCCCTATGA
1 TCGGGGTAAGAGATTGCTAATG-GTG--ATCTGCCCCAGGC
* * * *
297969 TCGGGATAAGAGATTGGATGATGGTGATCTACCCCAGGC
1 TCGGGGTAAGAGATT-GCTAATGGTGATCTGCCCCAGGC
* *
298008 TTGGGGTAAGAGA-T-CGAATGGTTGAAATCTGCCCCAGGC
1 TCGGGGTAAGAGATTGCTAATGG-TG--ATCTGCCCCAGGC
* *
298047 TCGCGTGTAAGAGATTTGCTAATGATGATCTGCCCCAGGC
1 TCG-GGGTAAGAGA-TTGCTAATGGTGATCTGCCCCAGGC
*
298087 TCGGGTGTAAGAGATTTGCTAATGATGATCTGCCCCAGGC
1 TCGGG-GTAAGAGA-TTGCTAATGGTGATCTGCCCCAGGC
** * * ** * *
298127 TCAAGGTAAGAGATCGACTGACT-GCAATTTGCCCTAGGC
1 TCGGGGTAAGAGATTG-CT-AATGGTGATCTGCCCCAGGC
* * *
298166 TTGGGGTAAGAGATTTGCTGATGGTGATCTGCCCCAAGC
1 TCGGGGTAAGAGA-TTGCTAATGGTGATCTGCCCCAGGC
*
298205 TCGGGGTAAGAGA-T-CGAATGGCTGCAATCTGCCCCAGGC
1 TCGGGGTAAGAGATTGCTAATGG-TG--ATCTGCCCCAGGC
* * * * *
298244 TCGAGGTAACAGATTTGCTGATGATGATCTGCCTCAGGC
1 TCGGGGTAAGAGA-TTGCTAATGGTGATCTGCCCCAGGC
** * * ** * * *
298283 TTAGGGTAAGAGATCGAAC-GATTATAATCTGCCCCAAGA
1 TCGGGGTAAGAGATTG--CTAATGGTGATCTGCCCCAGGC
* *
298322 TCGGGGTAAGAGATTGACTGATGATGATCTG-CCCAGGC
1 TCGGGGTAAGAGATTG-CTAATGGTGATCTGCCCCAGGC
* * * * * ** *
298360 TCAGGGTAAGAGA-T-CAAACGGCTACAATTTGCCTTAGGA
1 TCGGGGTAAGAGATTGCTAATGG-T--GATCTGCCCCAGGC
* * * * *
298399 TCGTGGTAAGAGATTGACTGATAGTGATCTACCCTAGGC
1 TCGGGGTAAGAGATTG-CTAATGGTGATCTGCCCCAGGC
* * * * *
298438 TAGGGGTAAGAGA-T-CGAATGGCTGCAATATGCCTCAAGC
1 TCGGGGTAAGAGATTGCTAATGG-TG--ATCTGCCCCAGGC
* * * * *
298477 TCGGGATAAGAGATTTGTTGATGGTGATCTACCTCAGGC
1 TCGGGGTAAGAGA-TTGCTAATGGTGATCTGCCCCAGGC
* * * * *
298516 TCGGGGTAAGAGATCGGTTGATGGTGATCTGTCTCAGGC
1 TCGGGGTAAGAGAT-TGCTAATGGTGATCTGCCCCAGGC
* * *
298555 TCGGGGTAAGAGA-T-CGAATGGCTGCAGTTTGCCTCAGGC
1 TCGGGGTAAGAGATTGCTAATGG-TG-A-TCTGCCCCAGGC
* *
298594 TCGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAGGC
1 TCGGGGTAAGAGA-TTGCTAATGGTGATCTGCCCCAGGC
* * * * *
298633 TTGGGGTAAGAGA-T-CGAACGACTGCAATCTGCCCCAGGA
1 TCGGGGTAAGAGATTGCTAATG-GTG--ATCTGCCCCAGGC
* ** * * *
298672 TCGAGAAAAGAGATTGATTGATGGTGATCTACCCCAGGC
1 TCGGGGTAAGAGATTG-CTAATGGTGATCTGCCCCAGGC
*
298711 TCGGGGTAAAAGAT
1 TCGGGGTAAGAGAT
298725 CAGATGACTA
Statistics
Matches: 591, Mismatches: 151, Indels: 106
0.70 0.18 0.12
Matches are distributed among these distances:
35 3 0.01
36 26 0.04
37 15 0.03
38 33 0.06
39 401 0.68
40 71 0.12
41 14 0.02
42 23 0.04
43 5 0.01
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.25
Consensus pattern (38 bp):
TCGGGGTAAGAGATTGCTAATGGTGATCTGCCCCAGGC
Found at i:297996 original size:78 final size:76
Alignment explanation
Indices: 297867--298101 Score: 272
Period size: 78 Copynumber: 3.0 Consensus size: 76
297857 TTATTGCCTG
* * *
297867 GAATGACTGCAATCTACCCTATGATCGGGGTAAGAGATTGACTAATGGTGATCTGCCCCAAGCTT
1 GAATGATTGCAATCTGCCCTATGATC-GGGTAAGAGATTGA-TAATGGTGATCTGCCCCAGGCTT
297932 GGGGTAAGAGATC
64 GGGGTAAGAGATC
* * *
297945 GAATGATTGCAATTTGCCCTATGATCGGGATAAGAGATTGGATGATGGTGATCTACCCCAGGCTT
1 GAATGATTGCAATCTGCCCTATGATCGGG-TAAGAGATT-GATAATGGTGATCTGCCCCAGGCTT
298010 GGGGTAAGAGATC
64 GGGGTAAGAGATC
* * * * * * *
298023 GAATGGTTGAAATCTGCCCCAGGCTCGCGTGTAAGAGATTTGCTAATGATGATCTGCCCCAGGCT
1 GAATGATTGCAATCTGCCCTATGATCG-G-GTAAGAGA-TTGATAATGGTGATCTGCCCCAGGCT
*
298088 CGGGTGTAAGAGAT
63 TGGG-GTAAGAGAT
298102 TTGCTAATGA
Statistics
Matches: 134, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
77 3 0.02
78 86 0.64
79 33 0.25
80 12 0.09
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (76 bp):
GAATGATTGCAATCTGCCCTATGATCGGGTAAGAGATTGATAATGGTGATCTGCCCCAGGCTTGG
GGTAAGAGATC
Found at i:298194 original size:78 final size:78
Alignment explanation
Indices: 298074--298531 Score: 453
Period size: 78 Copynumber: 5.9 Consensus size: 78
298064 GCTAATGATG
* *
298074 ATCTGCCCCAGGCTCGGGTGTAAGAGATTTGCTAATGATGATCTGCCCCAGGCTCAAGGTAAGAG
1 ATCTGCCCCAGGCTCGGG-GTAAGAGATTTGCTGATGATGATCTGCCCCAGGCTCAGGGTAAGAG
*
298139 ATCGACTGACTGCA
65 ATCGACTGGCTGCA
* * * * * *
298153 ATTTGCCCTAGGCTTGGGGTAAGAGATTTGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAGAGA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAGGCTCAGGGTAAGAGA
*
298218 TCGAATGGCTGCA
66 TCGACTGGCTGCA
* * * *
298231 ATCTGCCCCAGGCTCGAGGTAACAGATTTGCTGATGATGATCTGCCTCAGGCTTAGGGTAAGAGA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAGGCTCAGGGTAAGAGA
** **
298296 TCGAAC-GATTATA
66 TCG-ACTGGCTGCA
* *
298309 ATCTGCCCCAAGATCGGGGTAAGAGA-TTGACTGATGATGATCTG-CCCAGGCTCAGGGTAAGAG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTTG-CTGATGATGATCTGCCCCAGGCTCAGGGTAAGAG
* *
298372 ATCAAAC-GGCTACA
65 ATC-GACTGGCTGCA
* ** * * * *
298386 ATTTGCCTTAGGATCGTGGTAAGAGA-TTGACTGAT-AGTGATCTACCCTAGGCT-AGGGGTAAG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTTG-CTGATGA-TGATCTGCCCCAGGCTCA-GGGTAAG
*
298448 AGATCGAATGGCTGCA
63 AGATCGACTGGCTGCA
* * * * * * * * *
298464 ATATGCCTCAAGCTCGGGATAAGAGATTTGTTGATGGTGATCTACCTCAGGCTCGGGGTAAGAGA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAGGCTCAGGGTAAGAGA
298529 TCG
66 TCG
298532 GTTGATGGTG
Statistics
Matches: 313, Mismatches: 56, Indels: 21
0.80 0.14 0.05
Matches are distributed among these distances:
76 1 0.00
77 67 0.21
78 226 0.72
79 19 0.06
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (78 bp):
ATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAGGCTCAGGGTAAGAGA
TCGACTGGCTGCA
Found at i:298236 original size:197 final size:196
Alignment explanation
Indices: 297891--298296 Score: 564
Period size: 197 Copynumber: 2.1 Consensus size: 196
297881 TACCCTATGA
* *** *
297891 TCGGGGTAAGAGA-TTGACTAATGGTGATCTGCCCCAAGCTTGGGGTAAGAGATCGAATGATTGC
1 TCGGGGTAAGAGATTTGACTAATGATGATCTGCCCCAAGCTCAAGGTAAGAGATCGAATGACTGC
* * *
297955 AATTTGCCCTATGATCGGGATAAGAGATTGGATGATGGTGATCTACCCCAGGCTTGGGGTAAGAG
66 AATTTGCCCTAGGATCGGGATAAGAGATTGGATGATGGTGATCTACCCCAAGCTCGGGGTAAGAG
* * *
298020 ATCGAATGGTTGAAATCTGCCCCAGGCTCGCGTGTAAGAGATTTGCTAATGATGATCTGCCCCAG
131 ATCGAATGGCTGAAATCTGCCCCAGGCTCGAG-GTAACAGATTTGCTAATGATGATCTGCCCCAG
298085 GC
195 GC
* *
298087 TCGGGTGTAAGAGATTTG-CTAATGATGATCTGCCCCAGGCTCAAGGTAAGAGATCGACTGACTG
1 TCGGG-GTAAGAGATTTGACTAATGATGATCTGCCCCAAGCTCAAGGTAAGAGATCGAATGACTG
* * * * * *
298151 CAATTTGCCCTAGGCTTGGGGTAAGAGATTTGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAGA
65 CAATTTGCCCTAGGATCGGGATAAGAGATTGGATGATGGTGATCTACCCCAAGCTCGGGGTAAGA
* * *
298216 GATCGAATGGCTGCAATCTGCCCCAGGCTCGAGGTAACAGATTTGCTGATGATGATCTGCCTCAG
130 GATCGAATGGCTGAAATCTGCCCCAGGCTCGAGGTAACAGATTTGCTAATGATGATCTGCCCCAG
298281 GC
195 GC
**
298283 TTAGGGTAAGAGAT
1 TCGGGGTAAGAGAT
298297 CGAACGATTA
Statistics
Matches: 184, Mismatches: 24, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
195 9 0.05
196 39 0.21
197 133 0.72
198 3 0.02
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (196 bp):
TCGGGGTAAGAGATTTGACTAATGATGATCTGCCCCAAGCTCAAGGTAAGAGATCGAATGACTGC
AATTTGCCCTAGGATCGGGATAAGAGATTGGATGATGGTGATCTACCCCAAGCTCGGGGTAAGAG
ATCGAATGGCTGAAATCTGCCCCAGGCTCGAGGTAACAGATTTGCTAATGATGATCTGCCCCAGG
C
Found at i:298283 original size:117 final size:117
Alignment explanation
Indices: 298034--298646 Score: 466
Period size: 117 Copynumber: 5.2 Consensus size: 117
298024 AATGGTTGAA
* * * *
298034 ATCTGCCCCAGGCTCGCGTGTAAGAGATTTGCTAATGATGATCTGCCCCAGGCTCGGGTGTAAGA
1 ATCTGCCTCAGGCTCG-GGGTAAGAGATTTGCTGATGGTGATCTGCCCCAGGCTCGGG-GTAAGA
* * * *
298099 GATTTGCTAAT-GATG--ATCTGCCCCAGGCTCAAGGTAAGAGA-TCGACTGACTGCA--
64 GA--T-CGAATGGCTGCAATCTGCCCCAGGCTCGAGGTAAGAGATTTG-CTGA-TG-ATG
* * *
298153 ATTTGCC-CTAGGCTTGGGGTAAGAGATTTGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAGAG
1 ATCTGCCTC-AGGCTCGGGGTAAGAGATTTGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAGAG
*
298217 ATCGAATGGCTGCAATCTGCCCCAGGCTCGAGGTAACAGATTTGCTGATGATG
65 ATCGAATGGCTGCAATCTGCCCCAGGCTCGAGGTAAGAGATTTGCTGATGATG
** * ** * * *
298270 ATCTGCCTCAGGCTTAGGGTAAGAGA-TCGAAC-GATTATAATCTGCCCCAAGATCGGGGTAAGA
1 ATCTGCCTCAGGCTCGGGGTAAGAGATTTG--CTGATGGTGATCTGCCCCAGGCTCGGGGTAAGA
* * * *** * * **
298333 GATTGACT-GATG-ATGATCTG-CCCAGGCTC-AGGGTAAGAGATCAAACGGCT-ACA
64 GATCGAATGGCTGCA--ATCTGCCCCAGGCTCGA-GGTAAGAGAT-TTGCTGATGATG
* * * * * * * *
298386 ATTTGCCTTAGGATCGTGGTAAGAGA-TTGACTGATAGTGATCTACCCTAGGCTAGGGGTAAGAG
1 ATCTGCCTCAGGCTCGGGGTAAGAGATTTG-CTGATGGTGATCTGCCCCAGGCTCGGGGTAAGAG
* * * * *
298450 ATCGAATGGCTGCAATATGCCTCAAGCTCG-GGATAAGAGATTTGTTGATGGTG
65 ATCGAATGGCTGCAATCTGCCCCAGGCTCGAGG-TAAGAGATTTGCTGATGATG
* ** * * *
298503 ATCTACCTCAGGCTCGGGGTAAGAGATCGGTTGATGGTGATCTGTCTCAGGCTCGGGGTAAGAGA
1 ATCTGCCTCAGGCTCGGGGTAAGAGATTTGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAGAGA
* * * *
298568 TCGAATGGCTGCAGTTTGCCTCAGGCTCGGGGTAAGAGATTTGCTGATGATG
66 TCGAATGGCTGCAATCTGCCCCAGGCTCGAGGTAAGAGATTTGCTGATGATG
* *
298620 ATCTGCCCCAGGCTTGGGGTAAGAGAT
1 ATCTGCCTCAGGCTCGGGGTAAGAGAT
298647 CGAACGACTG
Statistics
Matches: 390, Mismatches: 81, Indels: 48
0.75 0.16 0.09
Matches are distributed among these distances:
114 4 0.01
115 9 0.02
116 85 0.22
117 234 0.60
118 46 0.12
119 12 0.03
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.25
Consensus pattern (117 bp):
ATCTGCCTCAGGCTCGGGGTAAGAGATTTGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAGAGA
TCGAATGGCTGCAATCTGCCCCAGGCTCGAGGTAAGAGATTTGCTGATGATG
Found at i:298449 original size:155 final size:155
Alignment explanation
Indices: 298074--298530 Score: 451
Period size: 155 Copynumber: 2.9 Consensus size: 155
298064 GCTAATGATG
* * * * * *
298074 ATCTGCCCCAGGCTCGGGTGTAAGAGATTTGCTAATGATGATCTGCCC-CAGGCTCAAGGTAAGA
1 ATCTGCCCCAGGATCGAG-GTAACAGATTTGCTGATGATGATCT-CCCTCAGGCTTAGGGTAAGA
* * * * * *
298138 GATCG-ACTGACTGCAATTTGCCCTAGGCTTGGGGTAAGAGATTTGCTGATGGTGATCTGCCCCA
64 GATCGAAC-GACTACAATATGCCCCAAGATCGGGGTAAGAGATTTGCTGATGGTGATCTG-CCCA
* * * *
298202 AGCTCGGGGTAAGAGATCGAATGGCTGCA
127 GGCTCGGGGTAAGAGATCAAACGGCTACA
* *
298231 ATCTGCCCCAGGCTCGAGGTAACAGATTTGCTGATGATGATCTGCCTCAGGCTTAGGGTAAGAGA
1 ATCTGCCCCAGGATCGAGGTAACAGATTTGCTGATGATGATCTCCCTCAGGCTTAGGGTAAGAGA
* * * *
298296 TCGAACGATTATAATCTGCCCCAAGATCGGGGTAAGAGA-TTGACTGATGATGATCTGCCCAGGC
66 TCGAACGACTACAATATGCCCCAAGATCGGGGTAAGAGATTTG-CTGATGGTGATCTGCCCAGGC
*
298360 TCAGGGTAAGAGATCAAACGGCTACA
130 TCGGGGTAAGAGATCAAACGGCTACA
* ** * *
298386 ATTTGCCTTAGGATCGTGGTAAGAGA-TTGACTGAT-AGTGATCTACCCT-AGGC-TAGGGGTAA
1 ATCTGCCCCAGGATCGAGGTAACAGATTTG-CTGATGA-TGATCT-CCCTCAGGCTTA-GGGTAA
* * * * * * * *
298447 GAGATCGAATGGCTGCAATATGCCTCAAGCTCGGGATAAGAGATTTGTTGATGGTGATCTACCTC
62 GAGATCGAACGACTACAATATGCCCCAAGATCGGGGTAAGAGATTTGCTGATGGTGATCTGCC-C
298512 AGGCTCGGGGTAAGAGATC
126 AGGCTCGGGGTAAGAGATC
298531 GGTTGATGGT
Statistics
Matches: 251, Mismatches: 40, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
154 6 0.02
155 121 0.48
156 105 0.42
157 19 0.08
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.25
Consensus pattern (155 bp):
ATCTGCCCCAGGATCGAGGTAACAGATTTGCTGATGATGATCTCCCTCAGGCTTAGGGTAAGAGA
TCGAACGACTACAATATGCCCCAAGATCGGGGTAAGAGATTTGCTGATGGTGATCTGCCCAGGCT
CGGGGTAAGAGATCAAACGGCTACA
Found at i:298561 original size:233 final size:233
Alignment explanation
Indices: 298068--298568 Score: 623
Period size: 233 Copynumber: 2.1 Consensus size: 233
298058 AGATTTGCTA
298068 ATGATGATCTGCCCCAGGCTCGGGTGTAAGAGATTTGCTAATGATGATCTGCCCCAGGCTCAAGG
1 ATGATGATCTGCCCCAGGCTCGGG-GTAAGAGA-TTGCTAATGATGATCTGCCCCAGGCTCAAGG
* * * * * *
298133 TAAGAGATCGACTGACTGCAATTTGCCCTAGGCTTGGGGTAAGAGATTTGCTGATGGTGATCTGC
64 TAAGAGATCAACTGACTACAATTTGCCCTAGGATCGGGGTAAGAGATTTGCTGATAGTGATCTAC
* * *
298198 CCCAAGCTCGGGGTAAGAGATCGAATGGCTGCAATCTGCCCCAGGCTCGAGGTAACAGATTTGCT
129 CCCAAGCTAGGGGTAAGAGATCGAATGGCTGCAATATGCCCCAAGCTCGAGGTAACAGATTTGCT
* *
298263 GATGATGATCTGCCTCAGGCTTAGGGTAAGAGATCGAACG
194 GATGATGATCTACCTCAGGCTCAGGGTAAGAGATCGAACG
* * * * * *
298303 ATTATAATCTGCCCCAAGATCGGGGTAAGAGATTGACTGATGATGATCTG-CCCAGGCTCAGGGT
1 ATGATGATCTGCCCCAGGCTCGGGGTAAGAGATTG-CTAATGATGATCTGCCCCAGGCTCAAGGT
* * *
298367 AAGAGATCAAAC-GGCTACAATTTGCCTTAGGATCGTGGTAAGAGA-TTGACTGATAGTGATCTA
65 AAGAGATC-AACTGACTACAATTTGCCCTAGGATCGGGGTAAGAGATTTG-CTGATAGTGATCTA
* * * *
298430 CCCTAGGCTAGGGGTAAGAGATCGAATGGCTGCAATATGCCTCAAGCTCG-GGATAAGAGATTTG
128 CCCCAAGCTAGGGGTAAGAGATCGAATGGCTGCAATATGCCCCAAGCTCGAGG-TAACAGATTTG
* * * ***
298494 TTGATGGTGATCTACCTCAGGCTCGGGGTAAGAGATCGGTTG
192 CTGATGATGATCTACCTCAGGCTCAGGGTAAGAGATCGAACG
* * *
298536 ATGGTGATCTGTCTCAGGCTCGGGGTAAGAGAT
1 ATGATGATCTGCCCCAGGCTCGGGGTAAGAGAT
298569 CGAATGGCTG
Statistics
Matches: 225, Mismatches: 37, Indels: 10
0.83 0.14 0.04
Matches are distributed among these distances:
232 5 0.02
233 177 0.79
234 23 0.10
235 20 0.09
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (233 bp):
ATGATGATCTGCCCCAGGCTCGGGGTAAGAGATTGCTAATGATGATCTGCCCCAGGCTCAAGGTA
AGAGATCAACTGACTACAATTTGCCCTAGGATCGGGGTAAGAGATTTGCTGATAGTGATCTACCC
CAAGCTAGGGGTAAGAGATCGAATGGCTGCAATATGCCCCAAGCTCGAGGTAACAGATTTGCTGA
TGATGATCTACCTCAGGCTCAGGGTAAGAGATCGAACG
Found at i:298647 original size:117 final size:117
Alignment explanation
Indices: 298162--298649 Score: 475
Period size: 117 Copynumber: 4.2 Consensus size: 117
298152 AATTTGCCCT
*
298162 AGGCTTGGGGTAAGAGATTTG-CTGATGGTGATCTGCCCCAAGCTCGGGGTAAGAGATCGAATGG
1 AGGCTTGGGGTAAGAGA-TCGACTGATGGTGATCTGCCCCAAGCTCGGGGTAAGAGATCGAATGG
* * *
298226 CTGCAATCTGCCCCAGGCTCGAGGTAACAGATTTGCTGATGATGATCTGCCTC
65 CTGCAATCTGCCTCAGGCTCGGGGTAAGAGATTTGCTGATGATGATCTGCCTC
* ** * * * *
298279 AGGCTTAGGGTAAGAGATCGAAC-GATTATAATCTGCCCCAAGATCGGGGTAAGAGATTGACT-G
1 AGGCTTGGGGTAAGAGATCG-ACTGATGGTGATCTGCCCCAAGCTCGGGGTAAGAGATCGAATGG
* * *** * * ** * *
298342 ATG-ATGATCTGCC-CAGGCTCAGGGTAAGAGATCAAACGGCT-ACAATTTGCCTT
65 CTGCA--ATCTGCCTCAGGCTCGGGGTAAGAGAT-TTGCTGATGATGATCTGCCTC
* * * * * * * * *
298395 AGGATCGTGGTAAGAGATTGACTGATAGTGATCTACCCTAGGCTAGGGGTAAGAGATCGAATGGC
1 AGGCTTGGGGTAAGAGATCGACTGATGGTGATCTGCCCCAAGCTCGGGGTAAGAGATCGAATGGC
* * * * * *
298460 TGCAATATGCCTCAAGCTCGGGATAAGAGATTTGTTGATGGTGATCTACCTC
66 TGCAATCTGCCTCAGGCTCGGGGTAAGAGATTTGCTGATGATGATCTGCCTC
* ** * * *
298512 AGGCTCGGGGTAAGAGATCGGTTGATGGTGATCTGTCTCAGGCTCGGGGTAAGAGATCGAATGGC
1 AGGCTTGGGGTAAGAGATCGACTGATGGTGATCTGCCCCAAGCTCGGGGTAAGAGATCGAATGGC
* * *
298577 TGCAGTTTGCCTCAGGCTCGGGGTAAGAGATTTGCTGATGATGATCTGCCCC
66 TGCAATCTGCCTCAGGCTCGGGGTAAGAGATTTGCTGATGATGATCTGCCTC
298629 AGGCTTGGGGTAAGAGATCGA
1 AGGCTTGGGGTAAGAGATCGA
298650 ACGACTGCAA
Statistics
Matches: 287, Mismatches: 74, Indels: 20
0.75 0.19 0.05
Matches are distributed among these distances:
115 3 0.01
116 81 0.28
117 201 0.70
118 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (117 bp):
AGGCTTGGGGTAAGAGATCGACTGATGGTGATCTGCCCCAAGCTCGGGGTAAGAGATCGAATGGC
TGCAATCTGCCTCAGGCTCGGGGTAAGAGATTTGCTGATGATGATCTGCCTC
Found at i:301035 original size:3 final size:3
Alignment explanation
Indices: 301027--301053 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
301017 AGTCATCCGT
301027 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
301054 AATATCATAA
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:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:308968 original size:30 final size:28
Alignment explanation
Indices: 308914--308990 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 28
308904 ATAAAGTTCG
**
308914 GGGGTAAAATGT-ATTTTTTGGAAGTTT
1 GGGGTAAAATGTAATTTTTAAGAAGTTT
308941 AGGGGTAAAAATGTAATTTTTAAGAAGTTT
1 -GGGGT-AAAATGTAATTTTTAAGAAGTTT
*
308971 GAGGGTTAAAATGTAGTTTT
1 G-GGG-TAAAATGTAATTTT
308991 GGAAATATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 5 0.12
29 8 0.19
30 28 0.67
31 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.27, T:0.40
Consensus pattern (28 bp):
GGGGTAAAATGTAATTTTTAAGAAGTTT
Found at i:311210 original size:17 final size:17
Alignment explanation
Indices: 311190--311224 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
311180 ACTTAAACTT
311190 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
311207 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
311224 T
1 T
311225 TTAAAATTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:311224 original size:24 final size:24
Alignment explanation
Indices: 311183--311231 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 24
311173 GACTTTTACT
311183 TAAACTTTAAATTTAAATTTAAAA
1 TAAACTTTAAATTTAAATTTAAAA
311207 TAAA-TTTAAATTTAAAATTTAAAA
1 TAAACTTTAAATTT-AAATTTAAAA
311231 T
1 T
311232 TAGGTTAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
TAAACTTTAAATTTAAATTTAAAA
Found at i:311232 original size:7 final size:6
Alignment explanation
Indices: 311182--311229 Score: 62
Period size: 6 Copynumber: 7.8 Consensus size: 6
311172 GGACTTTTAC
*
311182 TTAAACT TTAAAT TTAAAT TTAAA- ATAAAT TTAAAT TTAAAAT TTAAA
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TT-AAAT TTAAA
311230 ATTAGGTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
5 4 0.11
6 22 0.59
7 11 0.30
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (6 bp):
TTAAAT
Found at i:321662 original size:26 final size:26
Alignment explanation
Indices: 321633--321684 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
321623 AAAATGGGAT
321633 GAATTCATACAATGAAATTAGCAAAA
1 GAATTCATACAATGAAATTAGCAAAA
321659 GAATTCATACAATGAAATTAGCAAAA
1 GAATTCATACAATGAAATTAGCAAAA
321685 AAAAATGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.54, C:0.12, G:0.12, T:0.23
Consensus pattern (26 bp):
GAATTCATACAATGAAATTAGCAAAA
Found at i:322230 original size:16 final size:17
Alignment explanation
Indices: 322205--322237 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
322195 ATAACATGTT
322205 ATAAAATAAAA-AACAA
1 ATAAAATAAAATAACAA
*
322221 ATAAAGTAAAATAACAA
1 ATAAAATAAAATAACAA
322238 GAAAATAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (17 bp):
ATAAAATAAAATAACAA
Found at i:324857 original size:45 final size:45
Alignment explanation
Indices: 324806--324898 Score: 177
Period size: 45 Copynumber: 2.1 Consensus size: 45
324796 TATATATTAT
324806 TAATTTTAAAAAATTTAATGTCTAACGAAGAGTATATACGTGGAC
1 TAATTTTAAAAAATTTAATGTCTAACGAAGAGTATATACGTGGAC
*
324851 TAATTTTAAAAAATTTGATGTCTAACGAAGAGTATATACGTGGAC
1 TAATTTTAAAAAATTTAATGTCTAACGAAGAGTATATACGTGGAC
324896 TAA
1 TAA
324899 CATCTAGATG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (45 bp):
TAATTTTAAAAAATTTAATGTCTAACGAAGAGTATATACGTGGAC
Found at i:324983 original size:8 final size:8
Alignment explanation
Indices: 324970--325002 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
324960 TAAATAATAT
324970 AAATTTAA
1 AAATTTAA
324978 AAATTTAA
1 AAATTTAA
324986 AAA-TTAA
1 AAATTTAA
*
324993 AATTTTAA
1 AAATTTAA
325001 AA
1 AA
325003 TTAAAAAGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
7 6 0.26
8 17 0.74
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
AAATTTAA
Found at i:324992 original size:15 final size:15
Alignment explanation
Indices: 324974--325009 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
324964 TAATATAAAT
324974 TTAAAAATTTAAAAA
1 TTAAAAATTTAAAAA
*
324989 TT-AAAATTTTAAAA
1 TTAAAAATTTAAAAA
325003 TTAAAAA
1 TTAAAAA
325010 GTGACAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TTAAAAATTTAAAAA
Found at i:326011 original size:35 final size:35
Alignment explanation
Indices: 325965--326035 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
325955 GTATATTTCA
* *
325965 TTTAACTTGACTTGCAAGCAATCTCTTAGATTTTG
1 TTTAACTTGACTTGCAAGCAATCTCCTAGAATTTG
*
326000 TTTAACTTGACTTGCAATCAATCTCCTAGAATTTG
1 TTTAACTTGACTTGCAAGCAATCTCCTAGAATTTG
326035 T
1 T
326036 GTCACACAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (35 bp):
TTTAACTTGACTTGCAAGCAATCTCCTAGAATTTG
Found at i:326099 original size:29 final size:29
Alignment explanation
Indices: 326066--326124 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
326056 TCCACCTTGA
* *
326066 CACGAATTCTCAACGAACAAGTTCTTCAC
1 CACGAACTCTCAACGAACAAGTTCTCCAC
326095 CACGAACTCTCAACGAACAAGTTCTCCAC
1 CACGAACTCTCAACGAACAAGTTCTCCAC
326124 C
1 C
326125 TCTTCCACGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.34, C:0.36, G:0.10, T:0.20
Consensus pattern (29 bp):
CACGAACTCTCAACGAACAAGTTCTCCAC
Found at i:329806 original size:25 final size:25
Alignment explanation
Indices: 329767--329854 Score: 95
Period size: 25 Copynumber: 3.4 Consensus size: 25
329757 TTTGACTTAA
*
329767 ACGAGCCTAAATAGAATATCGCTCAT
1 ACGAGCC-AAATAGAATATTGCTCAT
* *
329793 ACGAGCCAAATAGAATATTACTCTT
1 ACGAGCCAAATAGAATATTGCTCAT
* * *
329818 ACGAGCTAGAGTCAAAATATTGCTCAT
1 ACGAGCCA-AAT-AGAATATTGCTCAT
329845 ACGAGCCAAA
1 ACGAGCCAAA
329855 CAAAATTTTA
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
25 22 0.44
26 10 0.20
27 18 0.36
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.23
Consensus pattern (25 bp):
ACGAGCCAAATAGAATATTGCTCAT
Found at i:329844 original size:52 final size:52
Alignment explanation
Indices: 329781--329935 Score: 152
Period size: 52 Copynumber: 3.0 Consensus size: 52
329771 GCCTAAATAG
* * * *
329781 AATATCGCTCATACGAGCCAAATAGAATATTACTCTTACGAGCTAGAGTCAA
1 AATATCGCTCATACGAGCCAAACAAAATATTACTCTTACGAGCCAGAATCAA
* * *
329833 AATATTGCTCATACGAGCCAAACAAAATTTTACTCTTATGAGCCAGAATCAA
1 AATATCGCTCATACGAGCCAAACAAAATATTACTCTTACGAGCCAGAATCAA
* * * * * * *
329885 AAT-TACGCTCTTACAAGCTAGACAGAAT-TACACTCTTACGAGCCAAAATCA
1 AATAT-CGCTCATACGAGCCAAACAAAATAT-TACTCTTACGAGCCAGAATCA
329936 GAATTTATTC
Statistics
Matches: 85, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.98
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.25
Consensus pattern (52 bp):
AATATCGCTCATACGAGCCAAACAAAATATTACTCTTACGAGCCAGAATCAA
Found at i:329847 original size:27 final size:25
Alignment explanation
Indices: 329767--329887 Score: 89
Period size: 25 Copynumber: 4.6 Consensus size: 25
329757 TTTGACTTAA
* *
329767 ACGAGCCTAAATAGAATATCGCTCAT
1 ACGAGCC-AAATAAAATATTGCTCAT
* * *
329793 ACGAGCCAAATAGAATATTACTCTT
1 ACGAGCCAAATAAAATATTGCTCAT
* *
329818 ACGAGCTAGAGTCAAAATATTGCTCAT
1 ACGAGCCA-AAT-AAAATATTGCTCAT
* * * *
329845 ACGAGCCAAACAAAATTTTACTCTT
1 ACGAGCCAAATAAAATATTGCTCAT
*
329870 ATGAGCCAGAATCAAAAT
1 ACGAGCCA-AAT-AAAAT
329888 TACGCTCTTA
Statistics
Matches: 75, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
25 40 0.53
26 12 0.16
27 23 0.31
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.25
Consensus pattern (25 bp):
ACGAGCCAAATAAAATATTGCTCAT
Found at i:329888 original size:27 final size:27
Alignment explanation
Indices: 329792--329941 Score: 96
Period size: 25 Copynumber: 5.8 Consensus size: 27
329782 ATATCGCTCA
* *
329792 TACGAGCCA-AAT-AGAATATTACTCT
1 TACGAGCCAGAATCAAAATTTTACTCT
* * * * *
329817 TACGAGCTAGAGTCAAAATATTGCTCA
1 TACGAGCCAGAATCAAAATTTTACTCT
329844 TACGAGCCA-AA-CAAAATTTTACTCT
1 TACGAGCCAGAATCAAAATTTTACTCT
* ***
329869 TATGAGCCAGAATCAAAATTACGCTCT
1 TACGAGCCAGAATCAAAATTTTACTCT
* * * **
329896 TACAAGCTAG-A-CAGAATTACACTCT
1 TACGAGCCAGAATCAAAATTTTACTCT
* *
329921 TACGAGCCAAAATCAGAATTT
1 TACGAGCCAGAATCAAAATTT
329942 ATTCTTTTTC
Statistics
Matches: 96, Mismatches: 23, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
25 46 0.48
26 7 0.07
27 43 0.45
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.26
Consensus pattern (27 bp):
TACGAGCCAGAATCAAAATTTTACTCT
Found at i:331734 original size:25 final size:25
Alignment explanation
Indices: 331696--331788 Score: 114
Period size: 25 Copynumber: 3.7 Consensus size: 25
331686 GGAGCGAATG
* * * *
331696 ATTCTGGCTCGCTCGTAACAGCGAT
1 ATTCTGTCTGGCTCGTAAGAGTGAT
* *
331721 ATTCTGTCTAGCTCGTAAGAGTAAT
1 ATTCTGTCTGGCTCGTAAGAGTGAT
*
331746 ATTTTGTCTGGCTCGTAAGAGTGAT
1 ATTCTGTCTGGCTCGTAAGAGTGAT
331771 ATTCTGTCTGGGCTCGTA
1 ATTCTGTCT-GGCTCGTA
331789 TGAGCTAAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
25 50 0.86
26 8 0.14
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.35
Consensus pattern (25 bp):
ATTCTGTCTGGCTCGTAAGAGTGAT
Found at i:350267 original size:18 final size:19
Alignment explanation
Indices: 350230--350271 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
350220 GCCTAAAAGG
* *
350230 AATTTTAATTTTTGTTTTC
1 AATTTTAATGTTTATTTTC
350249 AATTTTAA-GTTTATTTTC
1 AATTTTAATGTTTATTTTC
350267 -ATTTT
1 AATTTT
350272 TTTTATGCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 5 0.24
18 8 0.38
19 8 0.38
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.67
Consensus pattern (19 bp):
AATTTTAATGTTTATTTTC
Found at i:352306 original size:18 final size:19
Alignment explanation
Indices: 352259--352311 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
352249 ATATGAATTA
*
352259 TTTAA-TTAATAAATTGGG
1 TTTAATTTAATTAATTGGG
*
352277 TTTATTTTTAATTAATTGGG
1 TTTA-ATTTAATTAATTGGG
352297 -TTAATTTAATTAATT
1 TTTAATTTAATTAATT
352312 TGATCCATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 15 0.50
19 3 0.10
20 12 0.40
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (19 bp):
TTTAATTTAATTAATTGGG
Found at i:361367 original size:11 final size:11
Alignment explanation
Indices: 361331--361372 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
361321 ATAATATTAC
361331 TTTT-TTAATA
1 TTTTATTAATA
*
361341 TTTTAATAAGATA
1 TTTT-ATTA-ATA
361354 TTTTATTAATA
1 TTTTATTAATA
361365 TTTTATTA
1 TTTTATTA
361373 TAAATAGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 4 0.15
11 11 0.41
12 5 0.19
13 7 0.26
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (11 bp):
TTTTATTAATA
Found at i:366771 original size:18 final size:18
Alignment explanation
Indices: 366748--366784 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
366738 TTTAGTCCTT
366748 AAGCATAAAACATGCAAA
1 AAGCATAAAACATGCAAA
366766 AAGCATAAAACATGCAAA
1 AAGCATAAAACATGCAAA
366784 A
1 A
366785 TAACCATTTT
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:0.62, C:0.16, G:0.11, T:0.11
Consensus pattern (18 bp):
AAGCATAAAACATGCAAA
Found at i:366836 original size:22 final size:22
Alignment explanation
Indices: 366811--366856 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
366801 TAACTTACAC
366811 CAGCCGAACATCTATAGATGTT
1 CAGCCGAACATCTATAGATGTT
*
366833 CAGCCGAACATCTATAGGTGTT
1 CAGCCGAACATCTATAGATGTT
366855 CA
1 CA
366857 CCCAACACCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (22 bp):
CAGCCGAACATCTATAGATGTT
Found at i:366868 original size:21 final size:22
Alignment explanation
Indices: 366811--366868 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
366801 TAACTTACAC
*
366811 CAGCCGAACATCTATAGATGTT
1 CAGCCCAACATCTATAGATGTT
* *
366833 CAGCCGAACATCTATAGGTGTT
1 CAGCCCAACATCTATAGATGTT
*
366855 CA-CCCAACACCTAT
1 CAGCCCAACATCTAT
366869 TTGCAATTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 10 0.30
22 23 0.70
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (22 bp):
CAGCCCAACATCTATAGATGTT
Found at i:371853 original size:14 final size:14
Alignment explanation
Indices: 371834--371860 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
371824 CTCGTCTTAT
371834 TGCTTCGACATGGA
1 TGCTTCGACATGGA
371848 TGCTTCGACATGG
1 TGCTTCGACATGG
371861 TCTTGATTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.22, G:0.30, T:0.30
Consensus pattern (14 bp):
TGCTTCGACATGGA
Found at i:382568 original size:19 final size:19
Alignment explanation
Indices: 382525--382571 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
382515 TGTCTAAGTT
*
382525 GGTAAATTTAAAGCCAAGA
1 GGTAAAATTAAAGCCAAGA
**
382544 TATAAAATTAAAGCCAAGA
1 GGTAAAATTAAAGCCAAGA
382563 GGTAAAATT
1 GGTAAAATT
382572 GAGCCAATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.51, C:0.09, G:0.17, T:0.23
Consensus pattern (19 bp):
GGTAAAATTAAAGCCAAGA
Found at i:384413 original size:38 final size:38
Alignment explanation
Indices: 384366--384452 Score: 165
Period size: 38 Copynumber: 2.3 Consensus size: 38
384356 GATGTCACCG
*
384366 CAAAGATACCTTAACCTCGTACAAGTAATTTCACGCTA
1 CAAACATACCTTAACCTCGTACAAGTAATTTCACGCTA
384404 CAAACATACCTTAACCTCGTACAAGTAATTTCACGCTA
1 CAAACATACCTTAACCTCGTACAAGTAATTTCACGCTA
384442 CAAACATACCT
1 CAAACATACCT
384453 AGAAGCACCA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.38, C:0.29, G:0.08, T:0.25
Consensus pattern (38 bp):
CAAACATACCTTAACCTCGTACAAGTAATTTCACGCTA
Found at i:387065 original size:18 final size:18
Alignment explanation
Indices: 387039--387077 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
387029 ATTGGACCAA
*
387039 ATGCGATCACAAAATCAG
1 ATGCAATCACAAAATCAG
* *
387057 ATGCAATCATACAATCAG
1 ATGCAATCACAAAATCAG
387075 ATG
1 ATG
387078 TGCCACAAGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.21
Consensus pattern (18 bp):
ATGCAATCACAAAATCAG
Found at i:393767 original size:17 final size:17
Alignment explanation
Indices: 393742--393784 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
393732 ATGCATCTCA
*
393742 TTTAATTGTCATTGTAT
1 TTTAATTGTCATTGCAT
*
393759 TTTAGTTGTCATTGCAT
1 TTTAATTGTCATTGCAT
*
393776 TTTACTTGT
1 TTTAATTGT
393785 TAGTTCATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.19, C:0.09, G:0.14, T:0.58
Consensus pattern (17 bp):
TTTAATTGTCATTGCAT
Found at i:397182 original size:158 final size:157
Alignment explanation
Indices: 396885--397291 Score: 532
Period size: 158 Copynumber: 2.6 Consensus size: 157
396875 TACAGTTTCG
* * *
396885 GGTGTTGGTCTTAGATGTCTTACAGATGGCTGAGGTCCTGCATTGGTTATGGATTCCCTACAGCT
1 GGTGTTGGTCTTAGATGTCCTACAGATGGCTGAGGTCCTGCATTGGTTACGGATTCTCTACAGCT
* * * * * * *
396950 CGTGTAAGTAGCATCGTGTAGCCTAACATCTCGACCCATAGCTTGTGTGAGCAGGCCTATTTCAT
66 CATGTGAGCAGCATCGTGTAGCCTAACATCTCGACCCACAGCTCGTGTAAGCAGGCCTATTTCAC
* *
397015 AGCTCGTGTGTGCATTACAGGTTATAT
131 AGCTCGTGTGAGCATTACAAGTTATAT
* * *
397042 AGGTGTTGGTCTTAGATGTCCTACCGATGGCTGAGGTCCTGAAATGGTTACGGATTCT-TCACAG
1 -GGTGTTGGTCTTAGATGTCCTACAGATGGCTGAGGTCCTGCATTGGTTACGGATTCTCT-ACAG
*
397106 CTCATGTGAGCAGCATCGTGTAGCCTAACATCTCGACCTACAGCTCGTGTAAGCAGGCCTATTTC
64 CTCATGTGAGCAGCATCGTGTAGCCTAACATCTCGACCCACAGCTCGTGTAAGCAGGCCTATTTC
* *
397171 ACAGCTTGTGTGAGCATTTCAAGTTATAT
129 ACAGCTCGTGTGAGCATTACAAGTTATAT
** * * *
397200 GAGTGAAGGTCTTATATGTCCTACTGATGGCTGAGGTCCTGCATTGGTGGTAC--ATTCTCTAAA
1 G-GTGTTGGTCTTAGATGTCCTACAGATGGCTGAGGTCCTGCATTGGT--TACGGATTCTCTACA
397263 GCTCATGTGAGCAGCATCGTGTAGTCCTA
63 GCTCATGTGAGCAGCATCGTGTAG-CCTA
397292 TAGCTCATGT
Statistics
Matches: 218, Mismatches: 25, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
157 2 0.01
158 208 0.95
159 5 0.02
160 3 0.01
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.32
Consensus pattern (157 bp):
GGTGTTGGTCTTAGATGTCCTACAGATGGCTGAGGTCCTGCATTGGTTACGGATTCTCTACAGCT
CATGTGAGCAGCATCGTGTAGCCTAACATCTCGACCCACAGCTCGTGTAAGCAGGCCTATTTCAC
AGCTCGTGTGAGCATTACAAGTTATAT
Found at i:403541 original size:157 final size:158
Alignment explanation
Indices: 403241--403702 Score: 574
Period size: 157 Copynumber: 2.9 Consensus size: 158
403231 ACAGTTTCGA
* * * ** * ** *
403241 GTGCTGGTCTTGGTTGTCCTACCGATGGTTGAGGTCCTGTATTGGTTGCGGATTCTCCACAACTC
1 GTGCTAGTCTTAGATGTCCTACCGATGACTGAAGTCCTACATTGGTTGCAGATTCTCCACAACTC
* * *
403306 GTGTGAGCAGCATCGTGTAGCCTAACATCTCGACCCACAACTCATGTGGGCAGGCCCATTTCACA
66 GTGTGAGCAGCATCGTGTAGCCTAACATCTCGACCCACAGCTCATGTGAGAAGGCCCATTTCACA
* *
403371 ACTTGTGTGAGCATTACAGGTTATATGG
131 GCTTGTGTGAGCATTACAGGTTATATAG
* ** * *
403399 GT-CT-GATCTTAGATGTCCTACTGATGGGTGAAGTTCTACATTGGTTGCAGATTCTCCACAGCT
1 GTGCTAG-TCTTAGATGTCCTACCGATGACTGAAGTCCTACATTGGTTGCAGATTCTCCACAACT
*
403462 TGTGTGAGCAGCATCGTGTAGCCTAACATCTCGACCCACAGCTCATGTGAGAAGGCCCATTTCAC
65 CGTGTGAGCAGCATCGTGTAGCCTAACATCTCGACCCACAGCTCATGTGAGAAGGCCCATTTCAC
* *
403527 AGCTCGTGTGAGCATTACAGTTTATATAG
130 AGCTTGTGTGAGCATTACAGGTTATATAG
* * *
403556 GTGCTAGTCTTAGATGTCCTACCGATGACTGAGGTCCTGCATTGGTTGTAGATTCTCC-CTAACT
1 GTGCTAGTCTTAGATGTCCTACCGATGACTGAAGTCCTACATTGGTTGCAGATTCTCCAC-AACT
* * * *
403620 CATGTGAGTAACATCGTGTAGTCC-CACATCTCGACCCAAACAGCTCATGTGAGCAA-GCCCATT
65 CGTGTGAGCAGCATCGTGTAG-CCTAACATCTCGACCC--ACAGCTCATGTGAG-AAGGCCCATT
403683 TCACAGCTTGTGTGAGCATT
126 TCACAGCTTGTGTGAGCATT
403703 TTCCTGAGTA
Statistics
Matches: 264, Mismatches: 32, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
156 1 0.00
157 138 0.52
158 80 0.30
159 3 0.01
160 40 0.15
161 2 0.01
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.30
Consensus pattern (158 bp):
GTGCTAGTCTTAGATGTCCTACCGATGACTGAAGTCCTACATTGGTTGCAGATTCTCCACAACTC
GTGTGAGCAGCATCGTGTAGCCTAACATCTCGACCCACAGCTCATGTGAGAAGGCCCATTTCACA
GCTTGTGTGAGCATTACAGGTTATATAG
Found at i:419275 original size:53 final size:53
Alignment explanation
Indices: 419191--419439 Score: 322
Period size: 53 Copynumber: 4.7 Consensus size: 53
419181 TTGTGCCAAT
* *
419191 GATTAAAGGTCCGATGACTCTGTTTCATCGTGAGCTATATGAATCCTATTACA
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACA
* *
419244 GATAAAAGGTCCGATGACTCTGTGTCATCGTGTGTTATATGAATCCTATTACA
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACA
* * *
419297 AATTAAAGGTCCGATGACTATGTGTCATCATGAGTTATATGAATCCTATTAC-
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACA
* * * * * * **
419349 GAATTAAGGGTCCGATGACTTTGTGTCACCGTGAGATACACGAATCC-ATTATG
1 G-ATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACA
* *
419402 GATTAAAGGTTCGATGACTTTGTGTCATCGTGAGTTAT
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTAT
419440 CAAATGCGAA
Statistics
Matches: 171, Mismatches: 23, Indels: 5
0.86 0.12 0.03
Matches are distributed among these distances:
52 36 0.21
53 135 0.79
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (53 bp):
GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACA
Found at i:426554 original size:52 final size:53
Alignment explanation
Indices: 426368--426563 Score: 286
Period size: 53 Copynumber: 3.7 Consensus size: 53
426358 TTGTGCCAAA
* * *
426368 GATTAAAAGTCTGATGACTCTATGTCATCGTGAGTTATATGAATCCTATTACG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACG
*
426421 GATTAAAGGTCCGATGACTCTGTGTCATTGTGAGTTATATGAATCCTATTACG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACG
* * * * * * *
426474 GTTTAAGGGTCCAATGACTTTGTGTCATCGTGAGATACATGAATCC-ATTATG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACG
426526 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTAT
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTAT
426564 CAAATGTGAA
Statistics
Matches: 125, Mismatches: 18, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
52 37 0.30
53 88 0.70
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.35
Consensus pattern (53 bp):
GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACG
Found at i:428500 original size:52 final size:52
Alignment explanation
Indices: 428438--428620 Score: 262
Period size: 52 Copynumber: 3.5 Consensus size: 52
428428 ATTTAATTTA
*
428438 ATACTCACGATGACACATAGTCATCGGACC-CTTTAATCCGTAAAGGAATCAT
1 ATACTCACGATGACACATAGTCATCGGACCTC-ATAATCCGTAAAGGAATCAT
* * *
428490 ATACTCACGATGACACATAGTTATCGGACCTCATAATCTGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGAATCAT
* * *
428542 ATACTCACGACGACACATAGTCATTGGACCTCATAATCCGTAAATG-ATACAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGAAT-CAT
*
428594 ATACTCACAATGACACATAGTCATCGG
1 ATACTCACGATGACACATAGTCATCGG
428621 GCATTTTTCA
Statistics
Matches: 116, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
51 1 0.01
52 114 0.98
53 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGAATCAT
Found at i:434893 original size:21 final size:23
Alignment explanation
Indices: 434843--434895 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 23
434833 AATAGTGCAG
*
434843 ACTTCTACCGATACAAGTGACTT
1 ACTTCTACCGAAACAAGTGACTT
*
434866 --TTATACCGAAACAAGT-A-TT
1 ACTTCTACCGAAACAAGTGACTT
434885 ACTTCTACCGA
1 ACTTCTACCGA
434896 TACTAAAGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
19 2 0.08
20 1 0.04
21 22 0.88
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.30
Consensus pattern (23 bp):
ACTTCTACCGAAACAAGTGACTT
Found at i:435687 original size:52 final size:52
Alignment explanation
Indices: 435625--435755 Score: 208
Period size: 52 Copynumber: 2.5 Consensus size: 52
435615 ATGGAATTGA
*
435625 TCACGATGACACATGGTCATCAGACCTCATAATCCGTAAAGGACTCATATAC
1 TCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGACTCATATAC
* * *
435677 TCACGATGACACATAGTCATCTGACCTCATAATCTGTAAAGGATTCATATAC
1 TCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGACTCATATAC
* *
435729 TCAGGATGACACATAGTCATCGGACCT
1 TCACGATGACACATAGTCATCAGACCT
435756 TTTTCATTTA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (52 bp):
TCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGACTCATATAC
Found at i:436927 original size:53 final size:53
Alignment explanation
Indices: 436847--436952 Score: 176
Period size: 53 Copynumber: 2.0 Consensus size: 53
436837 TAAATATTAA
* * *
436847 AATAAATAAATTTATGACTCGACTCATCAGATTTGTGATCCCGAAATCACTGT
1 AATAAATAAATTTACGACTCAACTCATCAGATTTGTGATCCCAAAATCACTGT
*
436900 AATAAATAAATTTACGACTCAACTCATCAGATTTGTGATCCTAAAATCACTGT
1 AATAAATAAATTTACGACTCAACTCATCAGATTTGTGATCCCAAAATCACTGT
436953 TTTCGACACC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (53 bp):
AATAAATAAATTTACGACTCAACTCATCAGATTTGTGATCCCAAAATCACTGT
Found at i:446862 original size:17 final size:17
Alignment explanation
Indices: 446842--446881 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
446832 GACAATGTAG
446842 ATGCAGTGACAATAAAA
1 ATGCAGTGACAATAAAA
* * *
446859 ATGCAATGACATTAATA
1 ATGCAGTGACAATAAAA
446876 ATGCAG
1 ATGCAG
446882 GAAAAATTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.12, G:0.17, T:0.23
Consensus pattern (17 bp):
ATGCAGTGACAATAAAA
Found at i:474639 original size:18 final size:18
Alignment explanation
Indices: 474612--474647 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
474602 AGAAAGAAAG
*
474612 AAAGAGACATTGATGATT
1 AAAGAAACATTGATGATT
474630 AAAGAAACATTGATGATT
1 AAAGAAACATTGATGATT
474648 TCATGGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (18 bp):
AAAGAAACATTGATGATT
Found at i:476891 original size:14 final size:15
Alignment explanation
Indices: 476874--476910 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
476864 TATATATATC
476874 TTTTCTTTTCT-TCT
1 TTTTCTTTTCTCTCT
*
476888 TTTTCCTTTCTCTCT
1 TTTTCTTTTCTCTCT
476903 TTTT-TTTT
1 TTTTCTTTT
476911 TTTTATGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTCTTTTCTCTCT
Found at i:477496 original size:17 final size:16
Alignment explanation
Indices: 477471--477523 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
477461 TACAATGAAA
*
477471 AATGGAAATGCGATGAC
1 AATGAAAATGC-ATGAC
*
477488 AATGCAAATGCAGTGAC
1 AATGAAAATGCA-TGAC
*
477505 AATTAAAATGCAATGAC
1 AATGAAAATGC-ATGAC
477522 AA
1 AA
477524 AAGGGATGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
16 1 0.03
17 29 0.94
18 1 0.03
ACGTcount: A:0.47, C:0.13, G:0.21, T:0.19
Consensus pattern (16 bp):
AATGAAAATGCATGAC
Found at i:481700 original size:98 final size:99
Alignment explanation
Indices: 481525--481728 Score: 383
Period size: 98 Copynumber: 2.1 Consensus size: 99
481515 CAAAGTCACT
*
481525 TGCATCACACATCACTTCAAATGGTTGCGACCAATCCGGTGCAACGATAATGGGTGCCTTCACGA
1 TGCATCACACATCACTTCAAATGGTTGCGACCAATCCGATGCAACGATAATGGGTGCCTTCACGA
481590 GCTGCTTCTTTATTTGCATAAATGCATTCACACA
66 GCTGCTTCTTTATTTGCATAAATGCATTCACACA
*
481624 TGCATCACACATCACTTCAAATGGTTGCGACCAAT-CGATGTAACGATAATGGGTGCCTTCACGA
1 TGCATCACACATCACTTCAAATGGTTGCGACCAATCCGATGCAACGATAATGGGTGCCTTCACGA
481688 GCTGCTTCTTTATTTGCATAAATGCATTCACACA
66 GCTGCTTCTTTATTTGCATAAATGCATTCACACA
481722 TGCATCA
1 TGCATCA
481729 TCAAAAAGGA
Statistics
Matches: 103, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
98 68 0.66
99 35 0.34
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (99 bp):
TGCATCACACATCACTTCAAATGGTTGCGACCAATCCGATGCAACGATAATGGGTGCCTTCACGA
GCTGCTTCTTTATTTGCATAAATGCATTCACACA
Found at i:489241 original size:5 final size:5
Alignment explanation
Indices: 489228--489275 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
489218 TGCAACAAGA
* * *
489228 TTTAT TTTAC TTTA- TTTAT TTTAT TTTAT TTCAT TTTAT TTTAG TTTA
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
489276 ACATTTTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
4 4 0.11
5 34 0.89
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (5 bp):
TTTAT
Found at i:489246 original size:14 final size:14
Alignment explanation
Indices: 489227--489275 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
489217 ATGCAACAAG
*
489227 ATTTATTTTACTTT
1 ATTTATTTTATTTT
489241 ATTTATTTTATTTT
1 ATTTATTTTATTTT
489255 ATTTCATTTTATTTT
1 ATTT-ATTTTATTTT
489270 AGTTTA
1 A-TTTA
489276 ACATTTTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
14 17 0.53
15 12 0.38
16 3 0.09
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.71
Consensus pattern (14 bp):
ATTTATTTTATTTT
Found at i:492105 original size:21 final size:22
Alignment explanation
Indices: 492079--492130 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
492069 CTCTCTGGAA
492079 ACTTGTATCGA-TAGAA-AAGTC
1 ACTTGTATCGAGTAGAACAA-TC
*
492100 ACTTGTATC-AGTAGAACTATC
1 ACTTGTATCGAGTAGAACAATC
492121 ACTTGTATCG
1 ACTTGTATCG
492131 GTTGAAATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 1 0.04
21 25 0.93
22 1 0.04
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (22 bp):
ACTTGTATCGAGTAGAACAATC
Found at i:501831 original size:37 final size:38
Alignment explanation
Indices: 501790--501887 Score: 101
Period size: 38 Copynumber: 2.6 Consensus size: 38
501780 GTACATGTTC
501790 ATGCAGTGACATTCTTGAGTGCAA-TTGAAGAATACTT
1 ATGCAGTGACATTCTTGAGTGCAATTTGAAGAATACTT
** * * * *
501827 ATGCAGCAATAGTTCTGGA-TGTAATTTGAAGAATATTT
1 ATGCAGTGACA-TTCTTGAGTGCAATTTGAAGAATACTT
* *
501865 ATGTAGTGACATTCTTGTGTGCA
1 ATGCAGTGACATTCTTGAGTGCA
501888 TTTCGAAAAT
Statistics
Matches: 45, Mismatches: 13, Indels: 5
0.71 0.21 0.08
Matches are distributed among these distances:
37 17 0.38
38 28 0.62
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (38 bp):
ATGCAGTGACATTCTTGAGTGCAATTTGAAGAATACTT
Found at i:510224 original size:31 final size:31
Alignment explanation
Indices: 510187--510279 Score: 186
Period size: 31 Copynumber: 3.0 Consensus size: 31
510177 ATATCAGTGC
510187 AATAATGTCAGATCTATATACTAAAATAGTT
1 AATAATGTCAGATCTATATACTAAAATAGTT
510218 AATAATGTCAGATCTATATACTAAAATAGTT
1 AATAATGTCAGATCTATATACTAAAATAGTT
510249 AATAATGTCAGATCTATATACTAAAATAGTT
1 AATAATGTCAGATCTATATACTAAAATAGTT
510280 GATCCCACGA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (31 bp):
AATAATGTCAGATCTATATACTAAAATAGTT
Found at i:519557 original size:14 final size:15
Alignment explanation
Indices: 519526--519564 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
519516 GGCCTGAGAC
519526 CCATTGA-C-TTGAA
1 CCATTGACCGTTGAA
519539 CCATTGACCGTTG-A
1 CCATTGACCGTTGAA
519553 CCATTGACCGTT
1 CCATTGACCGTT
519565 AACTGTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.29
14 14 0.58
15 3 0.12
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.31
Consensus pattern (15 bp):
CCATTGACCGTTGAA
Found at i:522487 original size:37 final size:38
Alignment explanation
Indices: 522445--522542 Score: 128
Period size: 38 Copynumber: 2.6 Consensus size: 38
522435 GTACATGTTC
522445 ATGCAGCGACATTCCTGGGTGCAA-TTGAAGAATACTT
1 ATGCAGCGACATTCCTGGGTGCAATTTGAAGAATACTT
* * *
522482 ATGCAGCGATAGTT-CTGGATGCAATTTGAAGAATATTT
1 ATGCAGCGACA-TTCCTGGGTGCAATTTGAAGAATACTT
* *
522520 ATGCAGCGACAATCTTGGGTGCA
1 ATGCAGCGACATTCCTGGGTGCA
522543 TTCCGAAAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
37 20 0.39
38 31 0.61
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.29
Consensus pattern (38 bp):
ATGCAGCGACATTCCTGGGTGCAATTTGAAGAATACTT
Found at i:522605 original size:37 final size:37
Alignment explanation
Indices: 522564--522634 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
522554 TTCCTGCGGC
* * *
522564 GACAGGTTTGGGTGCAATCTAGAAGTGCTCATGCGAT
1 GACAGGTTTAGGCGCAATCTAGAAGTGCTAATGCGAT
*
522601 GACAGTTTTAGGCGCAATCTAGAAGTGCTAATGC
1 GACAGGTTTAGGCGCAATCTAGAAGTGCTAATGC
522635 AACGACATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.27
Consensus pattern (37 bp):
GACAGGTTTAGGCGCAATCTAGAAGTGCTAATGCGAT
Found at i:526770 original size:24 final size:24
Alignment explanation
Indices: 526732--526830 Score: 144
Period size: 24 Copynumber: 4.1 Consensus size: 24
526722 GTATACTGGT
* *
526732 TAACCATTTTAGGCTCATAAGAGC
1 TAACCATTCTGGGCTCATAAGAGC
526756 TAACCATTCTGGGCTCATAAGAGC
1 TAACCATTCTGGGCTCATAAGAGC
* *
526780 TAACCATTTTGGCCTCATAAGAGC
1 TAACCATTCTGGGCTCATAAGAGC
**
526804 TAACCATTCTGGGCTCATGTGAGC
1 TAACCATTCTGGGCTCATAAGAGC
526828 TAA
1 TAA
526831 TGTTGTTTAT
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 67 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.28
Consensus pattern (24 bp):
TAACCATTCTGGGCTCATAAGAGC
Found at i:526788 original size:48 final size:48
Alignment explanation
Indices: 526732--526830 Score: 164
Period size: 48 Copynumber: 2.1 Consensus size: 48
526722 GTATACTGGT
526732 TAACCATTTTAGG-CTCATAAGAGCTAACCATTCTGGGCTCATAAGAGC
1 TAACCATTTT-GGCCTCATAAGAGCTAACCATTCTGGGCTCATAAGAGC
**
526780 TAACCATTTTGGCCTCATAAGAGCTAACCATTCTGGGCTCATGTGAGC
1 TAACCATTTTGGCCTCATAAGAGCTAACCATTCTGGGCTCATAAGAGC
526828 TAA
1 TAA
526831 TGTTGTTTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
47 2 0.04
48 46 0.96
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.28
Consensus pattern (48 bp):
TAACCATTTTGGCCTCATAAGAGCTAACCATTCTGGGCTCATAAGAGC
Found at i:528442 original size:52 final size:52
Alignment explanation
Indices: 528364--528606 Score: 353
Period size: 52 Copynumber: 4.7 Consensus size: 52
528354 AATGAAAAAA
* * *
528364 AGGTCCGATGACTACGTATTATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCTGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
528416 AGGTCTGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCTGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * *
528468 AGGT-TCGATGACTACATGTCATCGTGAATATACGAATCCTTTACGAATTATG
1 AGGTCT-GATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * *
528520 AGGTCTGATAACTACGTGTCATCATGAGTATATGAATCCTTTACGGACTATG
1 AGGTCTGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * *
528572 AGGTCCGATGACTAGGTATCATCGTGAGTATATGA
1 AGGTCTGATGACTACGTGTCATCGTGAGTATATGA
528607 TTCTTTAACG
Statistics
Matches: 170, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
51 1 0.01
52 168 0.99
53 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (52 bp):
AGGTCTGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:528469 original size:26 final size:26
Alignment explanation
Indices: 528388--528469 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
528378 CGTATTATCG
528388 TGAGTATATGAATCCTTTACGGATTA
1 TGAGTATATGAATCCTTTACGGATTA
* * * * **
528414 TGAGGTCTGATGACTACGTGT-C--ATCG
1 TGA-GTAT-ATGAAT-CCTTTACGGATTA
528440 TGAGTATATGAATCCTTTACGGATTA
1 TGAGTATATGAATCCTTTACGGATTA
528466 TGAG
1 TGAG
528470 GTTCGATGAC
Statistics
Matches: 38, Mismatches: 12, Indels: 12
0.61 0.19 0.19
Matches are distributed among these distances:
23 3 0.08
24 6 0.16
25 3 0.08
26 14 0.37
27 3 0.08
28 6 0.16
29 3 0.08
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.35
Consensus pattern (26 bp):
TGAGTATATGAATCCTTTACGGATTA
Found at i:528549 original size:104 final size:104
Alignment explanation
Indices: 528364--528621 Score: 392
Period size: 104 Copynumber: 2.5 Consensus size: 104
528354 AATGAAAAAA
* * *
528364 AGGTCCGATGACTACGTATTATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCTGATGACT
1 AGGTCCGATGACTACGTATCATCGTGAGTATATGAATCCTTTACGAATTATGAGGTCTGATAACT
* *
528429 ACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
66 ACGTGTCATCATGAGTATATGAATCCTTTACGGACTATG
* * * * *
528468 AGGTTCGATGACTACATGTCATCGTGAATATACGAATCCTTTACGAATTATGAGGTCTGATAACT
1 AGGTCCGATGACTACGTATCATCGTGAGTATATGAATCCTTTACGAATTATGAGGTCTGATAACT
528533 ACGTGTCATCATGAGTATATGAATCCTTTACGGACTATG
66 ACGTGTCATCATGAGTATATGAATCCTTTACGGACTATG
* *
528572 AGGTCCGATGACTAGGTATCATCGTGAGTATATG-ATTCTTTAACGAATTA
1 AGGTCCGATGACTACGTATCATCGTGAGTATATGAATCCTTT-ACGAATTA
528622 AAGGTTTGAT
Statistics
Matches: 136, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
103 6 0.04
104 130 0.96
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (104 bp):
AGGTCCGATGACTACGTATCATCGTGAGTATATGAATCCTTTACGAATTATGAGGTCTGATAACT
ACGTGTCATCATGAGTATATGAATCCTTTACGGACTATG
Found at i:529040 original size:30 final size:30
Alignment explanation
Indices: 529004--529063 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
528994 AGATTATAGA
529004 CTTAAAAGCACTATGTAATTACTTGGAAAC
1 CTTAAAAGCACTATGTAATTACTTGGAAAC
*
529034 CTTAAAAGCACTTTGTAATTACTTGGAAAC
1 CTTAAAAGCACTATGTAATTACTTGGAAAC
529064 TATGTATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (30 bp):
CTTAAAAGCACTATGTAATTACTTGGAAAC
Found at i:531749 original size:21 final size:21
Alignment explanation
Indices: 531725--531774 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
531715 CCTATGACAG
* * * *
531725 TTCTACTGATACAAGTGAAGC
1 TTCTACTGAAACAAATCAAAC
531746 TTCTACTGAAACAAATCAAAC
1 TTCTACTGAAACAAATCAAAC
531767 TTCTACTG
1 TTCTACTG
531775 GTACTAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (21 bp):
TTCTACTGAAACAAATCAAAC
Found at i:537364 original size:195 final size:191
Alignment explanation
Indices: 537012--537368 Score: 482
Period size: 195 Copynumber: 1.8 Consensus size: 191
537002 TACTATAAAT
* *
537012 TGTTCCCTAACGATGCTGCTCACACGAGCTGTCAAGAGTATGCATAAGGCATAGTCCAAGCCATC
1 TGTTCCCTAACGATGCTGCTCACACGAGCTGTCAAGAATATGCATAAGGCATAATCCAAGCCATC
* * * *
537077 GTAGGGCCTATAATCCATTTAGGATCCATATCTCTTTTTCAACTCACGGTGCTGCTCACACGAGC
66 GTAGGGCCGATAATCCATTTAGGATCCATATCTCTTTCTCAACTCACGATGCTGCGCACACGAGC
*
537142 CGTCGAGGACTCGTAACATATGCGGTACCTCAACTATCGATACGATATCTGTGCATATAAC
131 CGTCAAGGACTCGTAACATATGCGGTACCTCAACTATCGATACGATATCTGTGCATATAAC
* * * *
537203 TGTTCCCTAATGATGCTGCTCACACGAGCTGTCGAGAATATGCACTTATGCATAAATCTC-AGCC
1 TGTTCCCTAACGATGCTGCTCACACGAGCTGTCAAGAATATGCA-TAAGGCAT-AATC-CAAGCC
* * * * * * **
537267 ATCGTATGGTCGATAATCCATTCTTGGATTCTTTTCTCATTTCTCGTCTCACGATGCTGCGCACA
63 ATCGTAGGGCCGATAATCCATT-TAGGATCCATATCTC-TTTCTCAACTCACGATGCTGCGCACA
*
537332 CGAGCTGTCAAGGACTCGTAACATATGCGGTACCTCA
126 CGAGCCGTCAAGGACTCGTAACATATGCGGTACCTCA
537369 GCCATTGCGT
Statistics
Matches: 141, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
191 41 0.29
192 6 0.04
193 26 0.18
194 12 0.09
195 56 0.40
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.29
Consensus pattern (191 bp):
TGTTCCCTAACGATGCTGCTCACACGAGCTGTCAAGAATATGCATAAGGCATAATCCAAGCCATC
GTAGGGCCGATAATCCATTTAGGATCCATATCTCTTTCTCAACTCACGATGCTGCGCACACGAGC
CGTCAAGGACTCGTAACATATGCGGTACCTCAACTATCGATACGATATCTGTGCATATAAC
Found at i:547822 original size:24 final size:24
Alignment explanation
Indices: 547773--547823 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
547763 ATAAAAAAAT
* **
547773 ATGACCAAGGAAGAATAATTTTAG
1 ATGAACAAGGAAGAATAATTCAAG
547797 ATGAACAAGGAAGAGA-AATTCAAG
1 ATGAACAAGGAAGA-ATAATTCAAG
547821 ATG
1 ATG
547824 CAGTAGCAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.49, C:0.08, G:0.24, T:0.20
Consensus pattern (24 bp):
ATGAACAAGGAAGAATAATTCAAG
Found at i:552524 original size:69 final size:70
Alignment explanation
Indices: 552442--552590 Score: 210
Period size: 69 Copynumber: 2.1 Consensus size: 70
552432 ATGAATAGGA
* * * * * *
552442 AATATTCTTTGCAAGAAAAAACAAAGTGAATAGTGAGATTCTCTGACGTGAACAGT-AAGATTCT
1 AATATTCTCTGCAAGAAAAAACAAAATGAACAATGAGATTCTCTGACGTAAACAATGAAGATTCT
* *
552506 TTGGC
66 CTGAC
552511 AATATTCTCTGCAAGAAAAAACAAAATGAACAATGAGATTCTCTGACGTAAACAATGAAGATTCT
1 AATATTCTCTGCAAGAAAAAACAAAATGAACAATGAGATTCTCTGACGTAAACAATGAAGATTCT
552576 CTGAC
66 CTGAC
*
552581 AAGATTCTCT
1 AATATTCTCT
552591 TATAATTTTA
Statistics
Matches: 70, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
69 50 0.71
70 20 0.29
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (70 bp):
AATATTCTCTGCAAGAAAAAACAAAATGAACAATGAGATTCTCTGACGTAAACAATGAAGATTCT
CTGAC
Found at i:552862 original size:14 final size:14
Alignment explanation
Indices: 552815--552862 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
552805 TTTAGCTTTC
552815 AAATTTAAGTTTTA
1 AAATTTAAGTTTTA
* *
552829 AAATTCAAATTTTA
1 AAATTTAAGTTTTA
*
552843 AAATTTAAGTTTTT
1 AAATTTAAGTTTTA
552857 AAATTT
1 AAATTT
552863 TAATTACATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (14 bp):
AAATTTAAGTTTTA
Found at i:552877 original size:22 final size:22
Alignment explanation
Indices: 552852--552895 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
552842 AAAATTTAAG
* *
552852 TTTTTAAATTTTAATTACATTA
1 TTTTCAAATTTGAATTACATTA
552874 TTTTCAAATTTGAATTACATTA
1 TTTTCAAATTTGAATTACATTA
552896 CAACTTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (22 bp):
TTTTCAAATTTGAATTACATTA
Found at i:552984 original size:14 final size:14
Alignment explanation
Indices: 552939--552986 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
552929 TTTAGCCTTC
552939 AAATTTAAGTTTTA
1 AAATTTAAGTTTTA
* **
552953 AAATTCAAAATTTA
1 AAATTTAAGTTTTA
*
552967 AAATTTAAGTTTTC
1 AAATTTAAGTTTTA
552981 AAATTT
1 AAATTT
552987 TAATTACATT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (14 bp):
AAATTTAAGTTTTA
Found at i:555150 original size:72 final size:71
Alignment explanation
Indices: 554988--555152 Score: 172
Period size: 72 Copynumber: 2.3 Consensus size: 71
554978 AAAACTTCAC
* * * *
554988 AAGTTAGTAACCAAGGTAAATTCTTCCCTAAACTTCTACCGACACCCTGTTGAATTGTTCTGAAA
1 AAGTTAGTAGCCAAGGTAACTTCTTCCCTAAACTTCTACCGACACCCTGATGAATTGTTCCGAAA
*
555053 CAACCC
66 CAACCA
* * * * * *
555059 AAGTCAATAGCC-AGAGTAACTTC-TCCCGTAGGACTTCTATCGATACCCTGATGAGTTGTTCCG
1 AAGTTAGTAGCCAAG-GTAACTTCTTCCC-TA-AACTTCTACCGACACCCTGATGAATTGTTCCG
* *
555122 AAACAGCTA
63 AAACAACCA
555131 AAGTTAGTAGCCAAGGTAACTT
1 AAGTTAGTAGCCAAGGTAACTT
555153 TTACTTGTAC
Statistics
Matches: 75, Mismatches: 15, Indels: 7
0.77 0.15 0.07
Matches are distributed among these distances:
70 6 0.08
71 18 0.24
72 49 0.65
73 2 0.03
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (71 bp):
AAGTTAGTAGCCAAGGTAACTTCTTCCCTAAACTTCTACCGACACCCTGATGAATTGTTCCGAAA
CAACCA
Found at i:556248 original size:18 final size:18
Alignment explanation
Indices: 556207--556251 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
556197 CTTATGAGCT
556207 AGTATGCTCTAATAGGCC
1 AGTATGCTCTAATAGGCC
*
556225 AATATGCTCTAACTA-GCC
1 AGTATGCTCTAA-TAGGCC
*
556243 CGTATGCTC
1 AGTATGCTC
556252 AAACGAGCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 21 0.91
19 2 0.09
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.29
Consensus pattern (18 bp):
AGTATGCTCTAATAGGCC
Found at i:562509 original size:15 final size:15
Alignment explanation
Indices: 562491--562570 Score: 65
Period size: 15 Copynumber: 5.3 Consensus size: 15
562481 GCACTCATGG
562491 TGCGAACACTGAAGT
1 TGCGAACACTGAAGT
*
562506 TGCGAGA-ACTGATGT
1 TGCGA-ACACTGAAGT
* *
562521 TGCGAGCACTCACA-T
1 TGCGAACACTGA-AGT
* *
562536 TGTGAACACTGATGT
1 TGCGAACACTGAAGT
* *
562551 TGCGAACACTCACGT
1 TGCGAACACTGAAGT
562566 TGCGA
1 TGCGA
562571 GCATGGATGA
Statistics
Matches: 50, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
15 49 0.98
16 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.24
Consensus pattern (15 bp):
TGCGAACACTGAAGT
Found at i:562527 original size:45 final size:45
Alignment explanation
Indices: 562478--562573 Score: 113
Period size: 45 Copynumber: 2.1 Consensus size: 45
562468 ATGGAAGATA
** * *
562478 CGAGCACTCATGGTGCGAACACTGAAGTTGCGAGA-ACTGATGTTG
1 CGAGCACTCACAGTGCGAACACTGAAGTTGCGA-ACACTCACGTTG
* * *
562523 CGAGCACTCACATTGTGAACACTGATGTTGCGAACACTCACGTTG
1 CGAGCACTCACAGTGCGAACACTGAAGTTGCGAACACTCACGTTG
562568 CGAGCA
1 CGAGCA
562574 TGGATGAAGG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 1 0.02
45 42 0.98
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (45 bp):
CGAGCACTCACAGTGCGAACACTGAAGTTGCGAACACTCACGTTG
Found at i:564229 original size:20 final size:19
Alignment explanation
Indices: 564192--564236 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
564182 TTTAGATATT
564192 AATTTTGGTAACTCCTTAG
1 AATTTTGGTAACTCCTTAG
*
564211 AAATTTTGGTAAAGT-CTTAG
1 -AATTTTGGT-AACTCCTTAG
564231 AATTTT
1 AATTTT
564237 TTTGTATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 6 0.26
20 14 0.61
21 3 0.13
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.44
Consensus pattern (19 bp):
AATTTTGGTAACTCCTTAG
Found at i:565393 original size:22 final size:23
Alignment explanation
Indices: 565368--565419 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
565358 ATCAAACTAT
* *
565368 AATATTTTATATTTTTA-CTCCA
1 AATATTTTATACTTTTATCTCAA
565390 AATATTTT-TACTTTTATCTCAA
1 AATATTTTATACTTTTATCTCAA
565412 AAT-TTTTA
1 AATATTTTA
565420 CTCCTTCCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.56
Consensus pattern (23 bp):
AATATTTTATACTTTTATCTCAA
Found at i:565412 original size:21 final size:21
Alignment explanation
Indices: 565368--565421 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
565358 ATCAAACTAT
*
565368 AATATTTTATATTTTTACTCCA
1 AATATTTT-TACTTTTACTCCA
565390 AATATTTTTACTTTTA-TCTCA
1 AATATTTTTACTTTTACTC-CA
565411 AA-ATTTTTACT
1 AATATTTTTACT
565422 CCTTCCCACT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 11 0.37
21 11 0.37
22 8 0.27
ACGTcount: A:0.31, C:0.13, G:0.00, T:0.56
Consensus pattern (21 bp):
AATATTTTTACTTTTACTCCA
Found at i:565925 original size:18 final size:18
Alignment explanation
Indices: 565881--565925 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
565871 CATTTTATAC
565881 TATTTATA-T-TATTGAA
1 TATTTATATTATATTGAA
*
565897 T-TGTATAATTATATTGAA
1 TATTTAT-ATTATATTGAA
565915 TATTTATATTA
1 TATTTATATTA
565926 AAATTGAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
15 4 0.17
16 2 0.09
17 1 0.04
18 12 0.52
19 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (18 bp):
TATTTATATTATATTGAA
Found at i:571812 original size:31 final size:29
Alignment explanation
Indices: 571768--571831 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 29
571758 AGGTTTGAAA
* *
571768 TTTGAAAGGATTTGAATAAAGATATTAAG
1 TTTGAAAGGATTTGAATAAAAAAATTAAG
*
571797 TTTGAAAATGGATTTGGATAAAAAAATTAAG
1 TTTG-AAA-GGATTTGAATAAAAAAATTAAG
571828 TTTG
1 TTTG
571832 TTTAAAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 4 0.13
30 3 0.10
31 23 0.77
ACGTcount: A:0.44, C:0.00, G:0.20, T:0.36
Consensus pattern (29 bp):
TTTGAAAGGATTTGAATAAAAAAATTAAG
Found at i:572911 original size:31 final size:29
Alignment explanation
Indices: 572874--572944 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 29
572864 TGTTTTAATA
*
572874 TAATATTAAATTGAAATTGTATAATATATTT
1 TAATATTAAATT-AAATT-AATAATATATTT
**
572905 TAATATTAAATTAAATTAATTTTATATTT
1 TAATATTAAATTAAATTAATAATATATTT
572934 TAATTATTAAA
1 TAA-TATTAAA
572945 CACATACTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 12 0.33
30 12 0.33
31 12 0.33
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (29 bp):
TAATATTAAATTAAATTAATAATATATTT
Found at i:573114 original size:11 final size:11
Alignment explanation
Indices: 573094--573125 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
573084 AACTAATTAA
573094 TTTAAATTATG
1 TTTAAATTATG
*
573105 TTTGAATTATG
1 TTTAAATTATG
573116 TTTAAATTAT
1 TTTAAATTAT
573126 TTAAAAGGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.56
Consensus pattern (11 bp):
TTTAAATTATG
Found at i:574149 original size:40 final size:40
Alignment explanation
Indices: 574075--574162 Score: 115
Period size: 40 Copynumber: 2.2 Consensus size: 40
574065 AAGGTATGTG
* *
574075 TATATATACAATATATTTGCATGAGTTTTGTTATATAATA
1 TATATATACAATATATATGCATGAGTCTTGTTATATAATA
* * *
574115 TATATATAC-ATATATATGTATGGGTCTTGATTATATACTA
1 TATATATACAATATATATGCATGAGTCTTG-TTATATAATA
574155 TATATATA
1 TATATATA
574163 TGTGTGTGTG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
39 16 0.38
40 26 0.62
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.47
Consensus pattern (40 bp):
TATATATACAATATATATGCATGAGTCTTGTTATATAATA
Found at i:575095 original size:17 final size:18
Alignment explanation
Indices: 575075--575114 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
575065 TTATATTGAA
*
575075 TGAACTG-TTATTTTATG
1 TGAACTGCTTATTCTATG
*
575092 TGAAATGCTTATTCTATG
1 TGAACTGCTTATTCTATG
575110 TGAAC
1 TGAAC
575115 CAGTTTTCGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.45
Consensus pattern (18 bp):
TGAACTGCTTATTCTATG
Found at i:579317 original size:7 final size:7
Alignment explanation
Indices: 579305--579335 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
579295 TTTATCAATT
579305 TTACATC
1 TTACATC
579312 TTACATC
1 TTACATC
*
579319 TTACATA
1 TTACATC
579326 TTACATC
1 TTACATC
579333 TTA
1 TTA
579336 ACTCTTTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.32, C:0.23, G:0.00, T:0.45
Consensus pattern (7 bp):
TTACATC
Found at i:587421 original size:21 final size:22
Alignment explanation
Indices: 587373--587421 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
587363 CAACATATAA
* * *
587373 ATATATTATTTTTTCTTCTTTT
1 ATATATTATTTATTATTATTTT
587395 AT-TATTA-TTATTATTATTTT
1 ATATATTATTTATTATTATTTT
587415 ATATATT
1 ATATATT
587422 TCTTGAGACA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 12 0.52
21 9 0.39
22 2 0.09
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (22 bp):
ATATATTATTTATTATTATTTT
Found at i:588938 original size:34 final size:34
Alignment explanation
Indices: 588895--588963 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
588885 TTCAGATGAT
588895 AGAATATTGCATCGACAATACATAAGTATGAATG
1 AGAATATTGCATCGACAATACATAAGTATGAATG
588929 AGAATATTGCATCGACAATACATAAGTATGAATG
1 AGAATATTGCATCGACAATACATAAGTATGAATG
588963 A
1 A
588964 ATAAGATTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.26
Consensus pattern (34 bp):
AGAATATTGCATCGACAATACATAAGTATGAATG
Found at i:595953 original size:26 final size:25
Alignment explanation
Indices: 595924--595976 Score: 88
Period size: 26 Copynumber: 2.1 Consensus size: 25
595914 TACCCTTACC
*
595924 AACCCATTTCTTTTAAACCCAAAATA
1 AACCCATTTCATTTAAACCC-AAATA
595950 AACCCATTTCATTTAAACCCAAATA
1 AACCCATTTCATTTAAACCCAAATA
595975 AA
1 AA
595977 AACCAAACCC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 7 0.27
26 19 0.73
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.28
Consensus pattern (25 bp):
AACCCATTTCATTTAAACCCAAATA
Found at i:613156 original size:21 final size:21
Alignment explanation
Indices: 613099--613158 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
613089 AATAATGCAG
613099 ACTTCTACCGAAACAAGTGAC
1 ACTTCTACCGAAACAAGTGAC
** *
613120 AGGTCTATC-AATACAAGTGAC
1 ACTTCTACCGAA-ACAAGTGAC
*
613141 TCTTCTACCGAAACAAGT
1 ACTTCTACCGAAACAAGT
613159 ATTACTTCTA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.37, C:0.25, G:0.15, T:0.23
Consensus pattern (21 bp):
ACTTCTACCGAAACAAGTGAC
Found at i:613960 original size:60 final size:60
Alignment explanation
Indices: 613844--613960 Score: 146
Period size: 60 Copynumber: 1.9 Consensus size: 60
613834 TTCAATTCAT
* * * * *
613844 ATTTGATACTCACGATGACACAGAGTCATCGAACCTTTAATCCGTAATGGGTTTCATTTA
1 ATTTAATACTCACGAAGACACAGAGTCACCGAACCTTTAATCCGTAATAGGATTCATTTA
* * *
613904 ATTTAATACTCACTAAGACACATAGTCACCGGACCTCTTAATCCGTAA-AGGATTCAT
1 ATTTAATACTCACGAAGACACAGAGTCACCGAACCT-TTAATCCGTAATAGGATTCAT
613961 ATACTCATGA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 37 0.77
61 11 0.23
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (60 bp):
ATTTAATACTCACGAAGACACAGAGTCACCGAACCTTTAATCCGTAATAGGATTCATTTA
Found at i:613989 original size:52 final size:52
Alignment explanation
Indices: 613909--614199 Score: 411
Period size: 52 Copynumber: 5.6 Consensus size: 52
613899 ATTTAATTTA
* * * *
613909 ATACTCACTAAGACACATAGTCACCGGACCTCTTAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
613961 ATACTCATGATGACACATAGTCATCGGACCTCATGATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* ** *
614013 ATACTCATGATGACACATAGTCATCGGGGCTCATAATTCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
614065 ATACTCACGATGACACATAGTCATCGAACCTCATAATTCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * * ** *
614117 ATACTAACGATGACATATAGACATCGGACCTCATAATCCAAAAAGTATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
614169 ATACTCACGATGACACATAGTCATCGAACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
614200 TTTTCATTTA
Statistics
Matches: 213, Mismatches: 26, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 213 1.00
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:619941 original size:12 final size:12
Alignment explanation
Indices: 619924--619973 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
619914 CAGGTTCTGT
619924 TTCTTCTTTCTC
1 TTCTTCTTTCTC
619936 TTCTTCCTTTC-C
1 TTCTT-CTTTCTC
*
619948 TTCTTCTTTTTC
1 TTCTTCTTTCTC
* *
619960 TTCATCCTTCTC
1 TTCTTCTTTCTC
619972 TT
1 TT
619974 GATCGCCTCC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 4 0.12
12 23 0.72
13 5 0.16
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64
Consensus pattern (12 bp):
TTCTTCTTTCTC
Found at i:621401 original size:24 final size:26
Alignment explanation
Indices: 621369--621417 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 26
621359 AAAGGTGGTC
621369 GGAGTGTTTTTGGAAG-A-GGGTTTA
1 GGAGTGTTTTTGGAAGCACGGGTTTA
621393 GGAGTGTTTTTGGAAGCACGGGTTT
1 GGAGTGTTTTTGGAAGCACGGGTTT
621418 TAGCCATGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 16 0.70
25 1 0.04
26 6 0.26
ACGTcount: A:0.18, C:0.04, G:0.41, T:0.37
Consensus pattern (26 bp):
GGAGTGTTTTTGGAAGCACGGGTTTA
Found at i:629210 original size:3 final size:3
Alignment explanation
Indices: 629202--629244 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
629192 CGGGGCAACA
*
629202 TCT TCT TCT TCT TTT TCT TCT TCT T-T TC- TCT TC- TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
629245 TTGCTTCAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 6 0.17
3 29 0.83
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TCT
Found at i:629225 original size:18 final size:18
Alignment explanation
Indices: 629202--629246 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
629192 CGGGGCAACA
*
629202 TCTTCTTCTTCT-TTTTCT
1 TCTTCTT-TTCTCTTCTCT
629220 TCTTCTTTTCTCTTCTCT
1 TCTTCTTTTCTCTTCTCT
629238 TCTTCTTTT
1 TCTTCTTTT
629247 GCTTCAATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (18 bp):
TCTTCTTTTCTCTTCTCT
Found at i:629251 original size:12 final size:11
Alignment explanation
Indices: 629204--629244 Score: 57
Period size: 10 Copynumber: 3.7 Consensus size: 11
629194 GGGCAACATC
629204 TTCTTCTTCTTT
1 TTCTTCTTC-TT
629216 TTCTTCTTCTT
1 TTCTTCTTCTT
*
629227 TTC-TCTTCTC
1 TTCTTCTTCTT
629237 TTCTTCTT
1 TTCTTCTT
629245 TTGCTTCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 9 0.33
11 9 0.33
12 9 0.33
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (11 bp):
TTCTTCTTCTT
Found at i:637049 original size:23 final size:24
Alignment explanation
Indices: 637003--637051 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
636993 GAGTTAAATT
*
637003 TGTCAGCACAAATATAATATAAAA
1 TGTCAGCACAAATATAATAGAAAA
637027 TGTCAG-AGCAAAT-TAATAGAAAA
1 TGTCAGCA-CAAATATAATAGAAAA
637050 TG
1 TG
637052 AATTGTTGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.24
Consensus pattern (24 bp):
TGTCAGCACAAATATAATAGAAAA
Done.