Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold30
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: 2650045
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.30
Warning! 144233 characters in sequence are not A, C, G, or T
File 3 of 17
Found at i:304763 original size:32 final size:32
Alignment explanation
Indices: 304695--304858 Score: 197
Period size: 32 Copynumber: 5.0 Consensus size: 32
304685 CACACCCAGA
* * *
304695 TGTATCGATACAT-TATGCTTTATATCAATACAT
1 TGTATCGATACATGT-T-CATTGTATCGATACAT
304728 TGTATCGATACATGTTCATTGTATCGATACAT
1 TGTATCGATACATGTTCATTGTATCGATACAT
*
304760 TGTATCGATATATGTTCATTGTATCGATACAT
1 TGTATCGATACATGTTCATTGTATCGATACAT
304792 TGTATCGATACATGTTCATTGTATCGATACA-
1 TGTATCGATACATGTTCATTGTATCGATACAT
* **
304823 TGTTCATTGTATACATGGACAATTGTATCGATACAT
1 TG-T-ATCG-ATACATGTTC-ATTGTATCGATACAT
304859 GAAACTGGCA
Statistics
Matches: 117, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
31 2 0.02
32 75 0.64
33 17 0.15
34 9 0.08
35 14 0.12
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATGTTCATTGTATCGATACAT
Found at i:304812 original size:51 final size:53
Alignment explanation
Indices: 304757--304859 Score: 158
Period size: 51 Copynumber: 2.0 Consensus size: 53
304747 TGTATCGATA
*
304757 CATTGTATCGATATATGTTCATTGTAT-CGAT-AC-ATTGTATCGATACATGTT
1 CATTGTATCGATACATGTTCATTGTATAC-ATGACAATTGTATCGATACATGTT
304808 CATTGTATCGATACATGTTCATTGTATACATGGACAATTGTATCGATACATG
1 CATTGTATCGATACATGTTCATTGTATACAT-GACAATTGTATCGATACATG
304860 AAACTGGCAG
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
51 28 0.60
52 1 0.02
53 2 0.04
54 16 0.34
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.40
Consensus pattern (53 bp):
CATTGTATCGATACATGTTCATTGTATACATGACAATTGTATCGATACATGTT
Found at i:306535 original size:9 final size:9
Alignment explanation
Indices: 306499--306534 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
306489 GTCAACCATC
306499 AATGATGAT
1 AATGATGAT
*
306508 AAAGATGAT
1 AATGATGAT
306517 AATGATGAT
1 AATGATGAT
*
306526 GATGATGAT
1 AATGATGAT
306535 GGTGACTCGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.44, C:0.00, G:0.25, T:0.31
Consensus pattern (9 bp):
AATGATGAT
Found at i:313912 original size:78 final size:79
Alignment explanation
Indices: 313777--314106 Score: 413
Period size: 79 Copynumber: 4.2 Consensus size: 79
313767 GCGATAATAA
* * * *
313777 CGGGGTTGGAGTATCCCCTCGAAAATAACGGAGTTGGAGTATCCCCGATTGTGAAAAATCGATGA
1 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCGATGT
313842 TTTAGAAATAAAAT
66 TTTAGAAATAAAAT
* * * *
313856 CGAGATTGGAGTAT-CCCTCGGAAATAACGGGGTTGGAGTATCCCCGACTATGAAAAATTGATGT
1 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCGATGT
313920 TTTAGAAATAAAAT
66 TTTAGAAATAAAAT
* * * * *
313934 TGGGGTTGGAGTATCCCCTCGAAAATAATGGGGTTAGAGTATCCCCGA-TA--AAAAATTGATGT
1 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCGATGT
313996 TTTAGAAATAAAAT
66 TTTAGAAATAAAAT
* * * * *
314010 CGGGGTTGGAGTGTCCCCTC-AGAAATAACAGGGTTGGAGTATCCCCGATTGTGAAAAGTC-AGT
1 CGGGATTGGAGTATCCCCTCGA-AAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCGA-T
*
314073 GTTTTGGAAATAAAAT
64 GTTTTAGAAATAAAAT
314089 C-GGAGTTGGAGTATCCCC
1 CGGGA-TTGGAGTATCCCC
314107 GATTATGGAA
Statistics
Matches: 219, Mismatches: 25, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
75 1 0.00
76 67 0.31
77 1 0.00
78 74 0.34
79 76 0.35
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (79 bp):
CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCGATGT
TTTAGAAATAAAAT
Found at i:313986 original size:28 final size:26
Alignment explanation
Indices: 313927--313986 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 26
313917 TGTTTTAGAA
*
313927 ATAAAATTGGGGTTGGAGTATCCCCTCG
1 ATAAAATTGGGGTTAGAGTAT-CCC-CG
*
313955 A-AAATAATGGGGTTAGAGTATCCCCG
1 ATAAA-ATTGGGGTTAGAGTATCCCCG
313981 ATAAAA
1 ATAAAA
313987 AATTGATGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
26 4 0.14
27 9 0.32
28 15 0.54
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (26 bp):
ATAAAATTGGGGTTAGAGTATCCCCG
Found at i:314170 original size:51 final size:51
Alignment explanation
Indices: 314042--314221 Score: 211
Period size: 51 Copynumber: 3.5 Consensus size: 51
314032 AAATAACAGG
* * *
314042 GTTGGAGTATCCCCGATTGTGAAAAGTCAGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATCGGTGTTTTGGAAATAAAATCGGA
* * *
314093 GTTGGAGTATCCCCGATTATGGAAAATGGGTGTTTTAGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATCGGTGTTTTGGAAATAAAATCGGA
* * * * **
314144 GTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATGAAA-CCAA
1 GTTGGAGTATCCCCGATTATGAAAAATCGGTGTTTTGGAAATAAAATCGGA
* *
314194 GATTCGAGTATCCCCGA-GATGAAAAATC
1 G-TTGGAGTATCCCCGATTATGAAAAATC
314222 AAGAAATTTA
Statistics
Matches: 110, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
50 11 0.10
51 99 0.90
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATCGGTGTTTTGGAAATAAAATCGGA
Found at i:314435 original size:16 final size:16
Alignment explanation
Indices: 314414--314449 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
314404 TTTCAAAGGG
314414 GGAATGAGATACCGTT
1 GGAATGAGATACCGTT
314430 GGAATGAGATACCGTT
1 GGAATGAGATACCGTT
314446 GGAA
1 GGAA
314450 AGATGACTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.33, C:0.11, G:0.33, T:0.22
Consensus pattern (16 bp):
GGAATGAGATACCGTT
Found at i:316552 original size:20 final size:20
Alignment explanation
Indices: 316523--316578 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
316513 AAAAATGCCT
* *
316523 AAATGCATCGATACATTGTA-
1 AAATGTATCGATACAATG-AG
316543 AAATGTATCGATACAATGAG
1 AAATGTATCGATACAATGAG
*
316563 CAATGTATCGATACAA
1 AAATGTATCGATACAA
316579 ATTGTGAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 1 0.03
20 31 0.97
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (20 bp):
AAATGTATCGATACAATGAG
Found at i:317240 original size:41 final size:40
Alignment explanation
Indices: 317159--317256 Score: 126
Period size: 41 Copynumber: 2.4 Consensus size: 40
317149 CTAGTTTTTA
* *
317159 AGGACAAAGGAAAAAAGAATGAAATAGGTCTTGCTCCTTG
1 AGGACAAAGGAAAAAGGAAAGAAATAGGTCTTGCTCCTTG
* *
317199 AGGACAAAGGAAGAAAGGAAAGGAA-AGTGTCTTGCTTCTTG
1 AGGACAAAGGAA-AAAGGAAAGAAATAG-GTCTTGCTCCTTG
317240 AGGACAAAGTGAAAAAG
1 AGGACAAAG-GAAAAAG
317257 AGTACGTTCA
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
40 14 0.27
41 34 0.67
42 3 0.06
ACGTcount: A:0.44, C:0.10, G:0.29, T:0.17
Consensus pattern (40 bp):
AGGACAAAGGAAAAAGGAAAGAAATAGGTCTTGCTCCTTG
Found at i:317493 original size:88 final size:88
Alignment explanation
Indices: 317344--318068 Score: 821
Period size: 88 Copynumber: 8.3 Consensus size: 88
317334 GAAGGGAATG
* * * *
317344 AAGTGTGTCCTGGTCTTTGAGGACAAA--AG-AAAGAAGGGAATGGAACGT--GTCTTGCTCTTT
1 AAGTGCGTCCTGCTCTTTGAGGACAAAGGGGAAAAGAAGGAAAT-GAA-GTGCGTCTTGCTCTTT
317404 GAGGACAAAGGAGAAAAGGAAAATA
64 GAGGACAAAGGAGAAAAGGAAAATA
* *
317429 AAGTGCGTCATGCTCTTTGAGGACAAAGGGGAAATGAAGGAAATGAAGTGCGTCTTGCTCTTTGA
1 AAGTGCGTCCTGCTCTTTGAGGACAAAGGGGAAAAGAAGGAAATGAAGTGCGTCTTGCTCTTTGA
*
317494 GGACAAGAGG-GAAGAGGAAAATA
66 GGACAA-AGGAGAAAAGGAAAATA
* * * * * * *
317517 AAGTGCGTCCTACTCTTTGAGGACAAAAGGGAAAAGAAGGGAATAAAGTGTGTCCTACTCTTTGA
1 AAGTGCGTCCTGCTCTTTGAGGACAAAGGGGAAAAGAAGGAAATGAAGTGCGTCTTGCTCTTTGA
*
317582 GGACAAAAGGAGAAAA-GAAGGGAATG
66 GGAC-AAAGGAGAAAAGGAA---AATA
* * * * * *
317608 GACTGTGTCCTGCTCTTTGAGGACAAAGGAGAAAAG--GAAAATAAAGT-CGTCTTGCTCTTTGA
1 AAGTGCGTCCTGCTCTTTGAGGACAAAGGGGAAAAGAAGGAAATGAAGTGCGTCTTGCTCTTTGA
317670 GGACAAAGGAGAAAAGGAAAATA
66 GGACAAAGGAGAAAAGGAAAATA
*
317693 AAGTGCGTCCTGCTCTTTGAGGACAAAGGGGAAATGAAGGAAATGAAGTGCGTCTTGCTCTTTGA
1 AAGTGCGTCCTGCTCTTTGAGGACAAAGGGGAAAAGAAGGAAATGAAGTGCGTCTTGCTCTTTGA
* * *
317758 GGACAAGGGGGAAGAGGAAAATA
66 GGACAAAGGAGAAAAGGAAAATA
* * * * *
317781 AAGTGCGTCCTGCTCTTTGAGGACAAAAGGGAAAAGAAGGGAATGAAGTGTGTCCTACTCTTTGA
1 AAGTGCGTCCTGCTCTTTGAGGACAAAGGGGAAAAGAAGGAAATGAAGTGCGTCTTGCTCTTTGA
* *
317846 GGACAAAAAGAGAAAA-GAAGGGAATG
66 GGAC-AAAGGAGAAAAGGAA---AATA
* * * * * * *
317872 GACTGTGTCCTGCTCTTTGAGGACAAAGGAGAAAAG--GAAAATAAAGT-TGTCTTGCTCTTTGA
1 AAGTGCGTCCTGCTCTTTGAGGACAAAGGGGAAAAGAAGGAAATGAAGTGCGTCTTGCTCTTTGA
317934 GGACAAAGGAGAAAAGGAAAATA
66 GGACAAAGGAGAAAAGGAAAATA
* * * * *
317957 AAGTGCGTCCTGCTCTTTGAGGACAAAAGTGAAAAAAAGGAAATGAAGTGCGTCCTGCTCTTTAA
1 AAGTGCGTCCTGCTCTTTGAGGACAAAGGGGAAAAGAAGGAAATGAAGTGCGTCTTGCTCTTTGA
* * *
318022 GGACAAGGGGGAAGAGGAAAATA
66 GGACAAAGGAGAAAAGGAAAATA
*
318045 AAGTGCGTCCTACTCTTTGAGGAC
1 AAGTGCGTCCTGCTCTTTGAGGAC
318069 TAGAAGGTGC
Statistics
Matches: 539, Mismatches: 78, Indels: 43
0.82 0.12 0.07
Matches are distributed among these distances:
85 91 0.17
86 2 0.00
87 43 0.08
88 303 0.56
89 33 0.06
91 67 0.12
ACGTcount: A:0.37, C:0.13, G:0.30, T:0.21
Consensus pattern (88 bp):
AAGTGCGTCCTGCTCTTTGAGGACAAAGGGGAAAAGAAGGAAATGAAGTGCGTCTTGCTCTTTGA
GGACAAAGGAGAAAAGGAAAATA
Found at i:317801 original size:264 final size:262
Alignment explanation
Indices: 317305--318068 Score: 1271
Period size: 264 Copynumber: 2.9 Consensus size: 262
317295 AACGAAATGC
* * * * * * *
317305 GTCCTGCTCTTTAAGGACAAAAAAGGAAAGAAGGGAATGAAGTGTGTCCTGGTCTTTGAGGACAA
1 GTCCTACTCTTTGAGGACAAAAGAGAAAAGAAGGGAATGGACTGTGTCCTGCTCTTTGAGGACAA
* * *
317370 AAGA-AAGAAGG-GAATGGAACGTGTCTTGCTCTTTGAGGACAAAGGAGAAAAGGAAAATAAAGT
66 AGGAGAA-AAGGAAAAT--AAAGTGTCTTGCTCTTTGAGGACAAAGGAGAAAAGGAAAATAAAGT
*
317433 GCGTCATGCTCTTTGAGGACAAAGGGGAAATGAAGGAAATGAAGTGCGTCTTGCTCTTTGAGGAC
128 GCGTCCTGCTCTTTGAGGACAAAGGGGAAATGAAGGAAATGAAGTGCGTCTTGCTCTTTGAGGAC
*
317498 AAGAGGGAAGAGGAAAATAAAGTGCGTCCTACTCTTTGAGGACAAAAGGGAAAAGAAGGGAATAA
193 AAGGGGGAAGAGGAAAATAAAGTGCGTCCTACTCTTTGAGGACAAAAGGGAAAAGAAGGGAATAA
317563 AGTGT
258 AGTGT
317568 GTCCTACTCTTTGAGGACAAAAGGAGAAAAGAAGGGAATGGACTGTGTCCTGCTCTTTGAGGACA
1 GTCCTACTCTTTGAGGACAAAA-GAGAAAAGAAGGGAATGGACTGTGTCCTGCTCTTTGAGGACA
317633 AAGGAGAAAAGGAAAATAAAGTCGTCTTGCTCTTTGAGGACAAAGGAGAAAAGGAAAATAAAGTG
65 AAGGAGAAAAGGAAAATAAAGT-GTCTTGCTCTTTGAGGACAAAGGAGAAAAGGAAAATAAAGTG
317698 CGTCCTGCTCTTTGAGGACAAAGGGGAAATGAAGGAAATGAAGTGCGTCTTGCTCTTTGAGGACA
129 CGTCCTGCTCTTTGAGGACAAAGGGGAAATGAAGGAAATGAAGTGCGTCTTGCTCTTTGAGGACA
* *
317763 AGGGGGAAGAGGAAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAAGGGAAAAGAAGGGAATGAA
194 AGGGGGAAGAGGAAAATAAAGTGCGTCCTACTCTTTGAGGACAAAAGGGAAAAGAAGGGAATAAA
317828 GTGT
259 GTGT
317832 GTCCTACTCTTTGAGGACAAAAAGAGAAAAGAAGGGAATGGACTGTGTCCTGCTCTTTGAGGACA
1 GTCCTACTCTTTGAGGAC-AAAAGAGAAAAGAAGGGAATGGACTGTGTCCTGCTCTTTGAGGACA
317897 AAGGAGAAAAGGAAAATAAAGTTGTCTTGCTCTTTGAGGACAAAGGAGAAAAGGAAAATAAAGTG
65 AAGGAGAAAAGGAAAATAAAG-TGTCTTGCTCTTTGAGGACAAAGGAGAAAAGGAAAATAAAGTG
* * ** * *
317962 CGTCCTGCTCTTTGAGGACAAAAGTGAAAAAAAGGAAATGAAGTGCGTCCTGCTCTTTAAGGACA
129 CGTCCTGCTCTTTGAGGACAAAGGGGAAATGAAGGAAATGAAGTGCGTCTTGCTCTTTGAGGACA
318027 AGGGGGAAGAGGAAAATAAAGTGCGTCCTACTCTTTGAGGAC
194 AGGGGGAAGAGGAAAATAAAGTGCGTCCTACTCTTTGAGGAC
318069 TAGAAGGTGC
Statistics
Matches: 474, Mismatches: 21, Indels: 11
0.94 0.04 0.02
Matches are distributed among these distances:
263 24 0.05
264 440 0.93
265 10 0.02
ACGTcount: A:0.37, C:0.13, G:0.30, T:0.20
Consensus pattern (262 bp):
GTCCTACTCTTTGAGGACAAAAGAGAAAAGAAGGGAATGGACTGTGTCCTGCTCTTTGAGGACAA
AGGAGAAAAGGAAAATAAAGTGTCTTGCTCTTTGAGGACAAAGGAGAAAAGGAAAATAAAGTGCG
TCCTGCTCTTTGAGGACAAAGGGGAAATGAAGGAAATGAAGTGCGTCTTGCTCTTTGAGGACAAG
GGGGAAGAGGAAAATAAAGTGCGTCCTACTCTTTGAGGACAAAAGGGAAAAGAAGGGAATAAAGT
GT
Found at i:318142 original size:60 final size:60
Alignment explanation
Indices: 318044--319051 Score: 1155
Period size: 60 Copynumber: 16.4 Consensus size: 60
318034 AGAGGAAAAT
* *
318044 AAAGTGCGTCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTT-GAAGGA
1 AAAG-GCGTCCTGCTCTTTGAGGACTA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* * * ** *
318105 GAAGGCGTCCTACTTTTTGAGGACTAAAAGGTGCCACCAACACGTGTGGGCTTTAAAAAGA
1 AAAGGCGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* *
318166 AAAGGCGTCCTACTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAG-GA
* * * *
318228 AAAGGCGTCCTGCTCTTTGAGGACTTGAGGGTGCCACCAACTCGTGTGGGCTTTGAAAGGA
1 AAAGGCGTCCTGCTCTTTGAGGAC-TAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* *
318289 AAAGGCGTCCTGCTCTTTGAAGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGA
* *** * * * * * *
318350 AAAAGAACCCTGCTCTTTAAGGACTGGAGGGTGCCACCACCTCGTGTAGGCTTTGAAAA-GA
1 AAAGGCGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGA
* * *
318411 AAAGGTGTCTTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAG--GA
** * *
318474 AAAGGCGTCCTGCTCTTTGAGGACTGGAGCGTGCCACCAACTCGTGTGGGCTTT-GAAGGA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAG-GTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* *
318534 GAAGGCATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
1 AAAGGCGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* * * *
318595 AAAGGCATCATGCTCTTTGAGGACTAAAGGCGCCACCAACTTCTGTGGGCTTTAAAAAGAAAAAA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAG------
*
318660 AA
59 GA
* ** * *
318662 AAAGGCGTCCTGCTTTTTGAGGACTAAAGGTGCCACCAACTCATGCGGGCTTT-GAAGGA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* * *
318721 GAAGGTGTCCTGCTCTTTGAGGACTAAAAGGTTCCACCAACTTGTGTGGGCTTTAAAAGGA
1 AAAGGCGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* * *
318782 GAAGGCGTCCTACTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAG-GA
* * * * *
318844 AAAGGCATCCTGCTCTTTGAGGACTGGAGGGTGCCACCAACTCGTGTGGGCTTT-GAAGGA
1 AAAGGCGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
*
318904 GAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAA-GGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* ** *
318965 AAAGGTGT-CTGCTCTTTGAGGACTAAAAAAAATGCCACCAACTTGTGTAGGCTTTAAAAGGA
1 AAAGGCGTCCTGCTCTTTGAGGACT---AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
*
319027 AAAGACGTCCTGCTCTTTGAGGACT
1 AAAGGCGTCCTGCTCTTTGAGGACT
319052 GTAGACACCT
Statistics
Matches: 806, Mismatches: 110, Indels: 60
0.83 0.11 0.06
Matches are distributed among these distances:
59 24 0.03
60 312 0.39
61 185 0.23
62 116 0.14
63 96 0.12
64 23 0.03
65 3 0.00
67 47 0.06
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.24
Consensus pattern (60 bp):
AAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
Found at i:318266 original size:123 final size:121
Alignment explanation
Indices: 318044--319051 Score: 1188
Period size: 123 Copynumber: 8.2 Consensus size: 121
318034 AGAGGAAAAT
* * * *
318044 AAAGTGCGTCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTT-GAAGGAGAA
1 AAAG-GCGTCCTGCTCTTTGAGGACTA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAA
* * * *
318108 GGCGTCCTACTTTTTGAGGACTAAAAGGTGCCACCAACACGTGTGGGCTTTAAAAAGA
64 GGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGGA
*
318166 AAAGGCGTCCTACTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAG-AAAAA
** * *
318231 GGCGTCCTGCTCTTTGAGGACTTGAGGGTGCCACCAACTCGTGTGGGCTTTGAAAGGA
64 GGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGGA
* *
318289 AAAGGCGTCCTGCTCTTTGAAGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAAG
*** * ** * * *
318354 GAACCCTGCTCTTTAAGGACTGGAGGGTGCCACCACCTCGTGTAGGCTTTGAAAA-GA
65 GCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTT-AAAAGGA
* *
318411 AAAGGTGTCTTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAG--AAAA
** *
318476 AGGCGTCCTGCTCTTTGAGGACT-GGAGCGTGCCACCAACTCGTGTGGGCTTT-GAAGGA
63 AGGCGTCCTGCTCTTTGAGGACTAAAAG-GTGCCACCAACTCGTGTGGGCTTTAAAAGGA
* * *
318534 GAAGGCATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
1 AAAGGCGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAG
* * * *
318599 GCATCATGCTCTTTGAGGACT-AAAGGCGCCACCAACTTC-TGTGGGCTTTAAAAAGAAAAAAAA
65 GCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAAC-TCGTGTGGGCTTT-AAAAG------GA
* ** * * * *
318662 AAAGGCGTCCTGCTTTTTGAGGACTAAAGGTGCCACCAACTCATGCGGGCTTT-GAAGGAGAAGG
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGG
* * *
318726 TGTCCTGCTCTTTGAGGACTAAAAGGTTCCACCAACTTGTGTGGGCTTTAAAAGGA
66 CGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGGA
* *
318782 GAAGGCGTCCTACTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAG-AAAAA
* ** * *
318847 GGCATCCTGCTCTTTGAGGACTGGAGGGTGCCACCAACTCGTGTGGGCTTT-GAAGGA
64 GGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGGA
* *
318904 GAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
1 AAAGGCGTCCTGCTCTTTGAGGACTAAA-GGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAG
* ** * *
318969 GTGT-CTGCTCTTTGAGGACTAAAAAAAATGCCACCAACTTGTGTAGGCTTTAAAAGGA
65 GCGTCCTGCTCTTTGAGGACT--AAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGGA
*
319027 AAAGACGTCCTGCTCTTTGAGGACT
1 AAAGGCGTCCTGCTCTTTGAGGACT
319052 GTAGACACCT
Statistics
Matches: 766, Mismatches: 93, Indels: 53
0.84 0.10 0.06
Matches are distributed among these distances:
120 111 0.14
121 57 0.07
122 180 0.23
123 243 0.32
124 72 0.09
126 32 0.04
127 48 0.06
128 23 0.03
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.24
Consensus pattern (121 bp):
AAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGG
CGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGGA
Found at i:319369 original size:13 final size:13
Alignment explanation
Indices: 319351--319375 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
319341 CATAAAGTGT
319351 TGTATCGATACAA
1 TGTATCGATACAA
319364 TGTATCGATACA
1 TGTATCGATACA
319376 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:319373 original size:33 final size:33
Alignment explanation
Indices: 319331--319397 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
319321 TTCAACGATT
319331 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
319364 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
319397 T
1 T
319398 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:319456 original size:13 final size:13
Alignment explanation
Indices: 319438--319475 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
319428 ATCACTTAAA
319438 TGTATCGATACAT
1 TGTATCGATACAT
319451 TGTATCGATACAT
1 TGTATCGATACAT
319464 TGTATCGATACA
1 TGTATCGATACA
319476 CTGATCTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:319542 original size:52 final size:52
Alignment explanation
Indices: 319484--319612 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
319474 CACTGATCTT
*
319484 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* **
319536 TGTATCGATACATGCAGGAAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
319588 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
319613 TCATATTTCG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:323751 original size:10 final size:10
Alignment explanation
Indices: 323736--323762 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
323726 TGCTAACTAA
323736 GTTTTTGTTT
1 GTTTTTGTTT
323746 GTTTTTGTTT
1 GTTTTTGTTT
323756 GTTTTTG
1 GTTTTTG
323763 CTTGATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (10 bp):
GTTTTTGTTT
Found at i:334501 original size:156 final size:157
Alignment explanation
Indices: 334159--334581 Score: 468
Period size: 155 Copynumber: 2.7 Consensus size: 157
334149 TAGTCCTAGG
** *
334159 GTATTTA-AGATAGGTTCATCCTGTCTT-TAATCTTTTTAAGTCTTTTAGGGTTATCGGGATACT
1 GTATTTAGA-ATAGGTTCATCCCAT-TTATAATCTTTTTAAGTCTTTTAGGGTTATCAGGATACT
* * * * * *
334222 TTCACGTCAAAGGTATACCCTTA-GGGTATTTTCATAATTTTTTA-AAATCGACTCTTACGTTTT
64 TTCACGTTAAAGGTATACCCTTAGGGGCATTTTCATAATTTTTTAGAACTCAACTCCTACGTTGT
* * *
334285 CACCGAGTCTGCTTTTATGCCGAATGTGA
129 CACCGAGTCTGATTTTATGCCAAAGGTGA
* * * * * * * * * *
334314 GCATTTAGGATAGGTTTATCTCA-TCATTAATCTTTTGAAGTCCTGTAAGGTTACCAGGATACTT
1 GTATTTAGAATAGGTTCATCCCATTTA-TAATCTTTTTAAGTCTTTTAGGGTTATCAGGATACTT
*
334378 TCACGTTAAAGGTATACCCTTAGGGGCATTTTCATAATTTTTTAGAACT-AACTCCTAGGTTGTC
65 TCACGTTAAAGGTATACCCTTAGGGGCATTTTCATAATTTTTTAGAACTCAACTCCTACGTTGTC
*
334442 ACCTAGTCTGATTTTATGCCAAAGGTGA
130 ACCGAGTCTGATTTTATGCCAAAGGTGA
* *
334470 GTATTTAGAATAGGTTCATCCCATTTATAATCCTTTTTAAGTCTTTTAGGGGTATCAGG-TCCTT
1 GTATTTAGAATAGGTTCATCCCATTTATAAT-CTTTTTAAGTCTTTTAGGGTTATCAGGATACTT
* * * *
334534 TTACGTTGAAA-GTATATCC-TAGGGGCATTTTCGTAATTTTTTTGAACT
65 TCACGTT-AAAGGTATACCCTTAGGGGCATTTTCATAATTTTTTAGAACT
334582 TAGTCCTTTA
Statistics
Matches: 220, Mismatches: 40, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
153 1 0.00
155 95 0.43
156 95 0.43
157 29 0.13
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (157 bp):
GTATTTAGAATAGGTTCATCCCATTTATAATCTTTTTAAGTCTTTTAGGGTTATCAGGATACTTT
CACGTTAAAGGTATACCCTTAGGGGCATTTTCATAATTTTTTAGAACTCAACTCCTACGTTGTCA
CCGAGTCTGATTTTATGCCAAAGGTGA
Found at i:338189 original size:166 final size:167
Alignment explanation
Indices: 337890--338240 Score: 467
Period size: 166 Copynumber: 2.1 Consensus size: 167
337880 GTAGGGACTA
* * *
337890 AAATAAAAATTTTCAAAAGTTTAGGGATTAAATAGCAAATTTTAGTTTTTAGAGTTAAAATCATC
1 AAATGAAAATTTTCAAAAGTTTAGGGATTAAATAGCAAATTTTAGTTTCTAGAGGTAAAATCATC
** ** * *
337955 ATTGAAATCATTTTTTTAGATTTCTATTATTCCTATGGTTTTCCTTAGAGGTATAGAAATTTTCA
66 ATTGAAATCATTTTTAAAGATTTCTATTATTCCTATGGCCTTCCTTAGAGGTATAGAAACTCTCA
* **
338020 AGACTTTTCGTATCCTCTTGGTTTTTCATTAGGTATG
131 AGACTTTTCATATCCTCTCAGTTTTTCATTAGGTATG
* *
338057 AAATGAAAATTTTCAAAA-TTTAGGGATTAAATAGTAAATTTTAGTTTCTAGAGGTAAAATCATT
1 AAATGAAAATTTTCAAAAGTTTAGGGATTAAATAGCAAATTTTAGTTTCTAGAGGTAAAATCATC
** * * *
338121 ATTTTAGTCATTTTTAAAGATTTCTATTATTCCTATGGCCTT-CTGTTGGGGTATA-AAAGCTCT
66 ATTGAAATCATTTTTAAAGATTTCTATTATTCCTATGGCCTTCCT-TAGAGGTATAGAAA-CTCT
* *
338184 CAAGACTTTTCATATCCTCTCATTTTTTCATTGGGTATG
129 CAAGACTTTTCATATCCTCTCAGTTTTTCATTAGGTATG
338223 AAATG-AAATTTTCAAAAG
1 AAATGAAAATTTTCAAAAG
338241 AGGGGCTTAA
Statistics
Matches: 160, Mismatches: 21, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
165 17 0.11
166 126 0.79
167 17 0.11
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (167 bp):
AAATGAAAATTTTCAAAAGTTTAGGGATTAAATAGCAAATTTTAGTTTCTAGAGGTAAAATCATC
ATTGAAATCATTTTTAAAGATTTCTATTATTCCTATGGCCTTCCTTAGAGGTATAGAAACTCTCA
AGACTTTTCATATCCTCTCAGTTTTTCATTAGGTATG
Found at i:340493 original size:20 final size:18
Alignment explanation
Indices: 340466--340518 Score: 70
Period size: 20 Copynumber: 2.8 Consensus size: 18
340456 CTGCCAGTTT
*
340466 CATGTATCGATACATGGCA
1 CATGTATCGATACAT-GAA
340485 CATTGTATCGATACAATGAA
1 CA-TGTATCGATAC-ATGAA
340505 CATGTATCGATACA
1 CATGTATCGATACA
340519 ATGTATCGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
18 1 0.03
19 13 0.42
20 15 0.48
21 2 0.06
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (18 bp):
CATGTATCGATACATGAA
Found at i:340512 original size:19 final size:19
Alignment explanation
Indices: 340466--340521 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
340456 CTGCCAGTTT
*
340466 CATGTATCGATAC-ATGGCA
1 CATGTATCGATACAAT-GAA
340485 CATTGTATCGATACAATGAA
1 CA-TGTATCGATACAATGAA
340505 CATGTATCGATACAATG
1 CATGTATCGATACAATG
340522 TATCGATACA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 17 0.50
20 15 0.44
21 2 0.06
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:340524 original size:13 final size:13
Alignment explanation
Indices: 340506--340531 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
340496 TACAATGAAC
340506 ATGTATCGATACA
1 ATGTATCGATACA
340519 ATGTATCGATACA
1 ATGTATCGATACA
340532 TTTGAGTGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:341120 original size:30 final size:31
Alignment explanation
Indices: 341084--341141 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
341074 TAAGGCTCTC
341084 ATTAAAAA-AATTTCTCCCCCTTGATAATCG
1 ATTAAAAAGAATTTCTCCCCCTTGATAATCG
*
341114 ATTAAAAAGATTTTCTCCCCCTTGATAA
1 ATTAAAAAGAATTTCTCCCCCTTGATAA
341142 AAATTTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 8 0.31
31 18 0.69
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.34
Consensus pattern (31 bp):
ATTAAAAAGAATTTCTCCCCCTTGATAATCG
Found at i:342572 original size:19 final size:19
Alignment explanation
Indices: 342548--342597 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
342538 AAATCGTAAC
342548 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
342567 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
342586 TGTATCGATACA
1 TGTATCGATACA
342598 ATGTATCGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:342604 original size:13 final size:13
Alignment explanation
Indices: 342586--342623 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
342576 ACATAAGTGT
342586 TGTATCGATACAA
1 TGTATCGATACAA
*
342599 TGTATCGACACAA
1 TGTATCGATACAA
342612 TGTATCGATACA
1 TGTATCGATACA
342624 TAAGTTTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:343654 original size:13 final size:13
Alignment explanation
Indices: 343636--343660 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
343626 CATAAAATGT
343636 TGTATCGATACAA
1 TGTATCGATACAA
343649 TGTATCGATACA
1 TGTATCGATACA
343661 TATTTTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:343742 original size:13 final size:13
Alignment explanation
Indices: 343724--343748 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
343714 ATTACTCAAA
343724 TGTATCGATACAT
1 TGTATCGATACAT
343737 TGTATCGATACA
1 TGTATCGATACA
343749 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:343812 original size:51 final size:51
Alignment explanation
Indices: 343757--343880 Score: 203
Period size: 52 Copynumber: 2.4 Consensus size: 51
343747 CACTGATCTT
*
343757 TGTATCGATACATGCAGGCAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAATTTGCCCAGATGTATCGATACACTATAAAA
* *
343808 TGTATCGATACATGCAGGTAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGG-CAATTTGCCCAGATGTATCGATACACTATAAAA
*
343860 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
343881 CTTTTCATAT
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
51 20 0.30
52 47 0.70
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (51 bp):
TGTATCGATACATGCAGGCAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:350077 original size:22 final size:21
Alignment explanation
Indices: 350042--350091 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
350032 TTTGTTGATG
*
350042 ATTTTG-A-TGAAAAATGAAGT
1 ATTTTGAAGTGAAAAAT-AAGA
350062 ATTTTGAAGTGAAAAATAAGA
1 ATTTTGAAGTGAAAAATAAGA
*
350083 AATTTGAAG
1 ATTTTGAAG
350092 AAGATTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 12 0.46
22 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAATAAGA
Found at i:350088 original size:21 final size:22
Alignment explanation
Indices: 350049--350091 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
350039 ATGATTTTGA
* *
350049 TGAAAAATGAAGTATTTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
350071 TGAAAAAT-AAGAAATTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
350092 AAGATTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (22 bp):
TGAAAAATGAAGAAATTTGAAG
Found at i:356469 original size:19 final size:19
Alignment explanation
Indices: 356425--356480 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
356415 CTACCAGTTT
**
356425 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
356445 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
356464 CATGTACCGATACAATG
1 CATGTATCGATACAATG
356481 TATCGATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:356487 original size:32 final size:32
Alignment explanation
Indices: 356446--356509 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
356436 ACAATTGTCC
*
356446 ATGTATCGATACAATGAACATGTACCGATACA
1 ATGTATCGATACAAAGAACATGTACCGATACA
* * *
356478 ATGTATCGATACAAAGCATATGTATCGATACA
1 ATGTATCGATACAAAGAACATGTACCGATACA
356510 TTTAAGTGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.27
Consensus pattern (32 bp):
ATGTATCGATACAAAGAACATGTACCGATACA
Found at i:359125 original size:20 final size:21
Alignment explanation
Indices: 359100--359147 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
359090 TTTGTTGATG
359100 ATTTTGATG-AAAAATAGAA-A
1 ATTTTGATGTAAAAAT-GAAGA
*
359120 ATTTTGATGTGAAAATGAAGA
1 ATTTTGATGTAAAAATGAAGA
359141 ATTTTGA
1 ATTTTGA
359148 AACAGATTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.46, C:0.00, G:0.19, T:0.35
Consensus pattern (21 bp):
ATTTTGATGTAAAAATGAAGA
Found at i:369419 original size:3 final size:3
Alignment explanation
Indices: 369411--369441 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
369401 CCAAAGCGAA
369411 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
369442 GTGGGTAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:373910 original size:20 final size:20
Alignment explanation
Indices: 373887--373930 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
373877 GGTTGTATTA
* *
373887 ATACAATGCAATTTGTATCG
1 ATACAATGAAAATTGTATCG
*
373907 ATAC-ATTAAAATTGTATCG
1 ATACAATGAAAATTGTATCG
373926 ATACA
1 ATACA
373931 TTACACCTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (20 bp):
ATACAATGAAAATTGTATCG
Found at i:375737 original size:18 final size:18
Alignment explanation
Indices: 375714--375751 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
375704 CAGGTTTAAA
375714 TTTGCCCTCCTTTTGGTT
1 TTTGCCCTCCTTTTGGTT
375732 TTTGCCCTCCTTTTGGTT
1 TTTGCCCTCCTTTTGGTT
375750 TT
1 TT
375752 GATATAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.00, C:0.26, G:0.16, T:0.58
Consensus pattern (18 bp):
TTTGCCCTCCTTTTGGTT
Found at i:376460 original size:111 final size:111
Alignment explanation
Indices: 376266--376499 Score: 468
Period size: 111 Copynumber: 2.1 Consensus size: 111
376256 ATATATCAAA
376266 GTATCGATACATAGGTATTTGTATCGATACATTAAGGTTGACTTAGGACAAAATTGTCAAAACCC
1 GTATCGATACATAGGTATTTGTATCGATACATTAAGGTTGACTTAGGACAAAATTGTCAAAACCC
376331 TTAAAAGTATCGATACACAATTCAAAGTATCGATACATGTTGCAAT
66 TTAAAAGTATCGATACACAATTCAAAGTATCGATACATGTTGCAAT
376377 GTATCGATACATAGGTATTTGTATCGATACATTAAGGTTGACTTAGGACAAAATTGTCAAAACCC
1 GTATCGATACATAGGTATTTGTATCGATACATTAAGGTTGACTTAGGACAAAATTGTCAAAACCC
376442 TTAAAAGTATCGATACACAATTCAAAGTATCGATACATGTTGCAAT
66 TTAAAAGTATCGATACACAATTCAAAGTATCGATACATGTTGCAAT
376488 GTATCGATACAT
1 GTATCGATACAT
376500 GCAAAAGATG
Statistics
Matches: 123, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 123 1.00
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (111 bp):
GTATCGATACATAGGTATTTGTATCGATACATTAAGGTTGACTTAGGACAAAATTGTCAAAACCC
TTAAAAGTATCGATACACAATTCAAAGTATCGATACATGTTGCAAT
Found at i:376597 original size:21 final size:20
Alignment explanation
Indices: 376551--376603 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
376541 GTAGCCAAAC
**
376551 TTGTATCGATACACCAAGTA
1 TTGTATCGATACACCAAAAA
376571 -TGTATCGATACACCAAAAAA
1 TTGTATCGATACACC-AAAAA
376591 TTGTATCGATACA
1 TTGTATCGATACA
376604 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 14 0.48
20 3 0.10
21 12 0.41
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (20 bp):
TTGTATCGATACACCAAAAA
Found at i:382169 original size:13 final size:13
Alignment explanation
Indices: 382151--382189 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
382141 ACATTTTTCT
382151 TTGTATCGATACA
1 TTGTATCGATACA
382164 TTGTATCGATACA
1 TTGTATCGATACA
* *
382177 CTGTATCAATACA
1 TTGTATCGATACA
382190 GAGGGATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:384661 original size:20 final size:19
Alignment explanation
Indices: 384606--384661 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
384596 AAAACCCTTA
*
384606 AAAGTATCGATACATAATTC
1 AAAGTATCGATACAT-GTTC
384626 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
384646 AATGTATCGATACATG
1 AAAGTATCGATACATG
384662 CAAAAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:384749 original size:13 final size:13
Alignment explanation
Indices: 384731--384756 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
384721 TACACCAAGT
384731 ATGTATCGATACA
1 ATGTATCGATACA
384744 ATGTATCGATACA
1 ATGTATCGATACA
384757 CCAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:384775 original size:34 final size:32
Alignment explanation
Indices: 384713--384777 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
384703 TAGCCAAACT
**
384713 TGTATCGATACACCAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAATGTATCGATACAA
384745 TGTATCGATACACCAAAAAATTGTATCGATACA
1 TGTATCGATACACC-AAAAA-TGTATCGATACA
384778 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 14 0.48
33 3 0.10
34 12 0.41
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACCAAAAATGTATCGATACAA
Found at i:386042 original size:21 final size:22
Alignment explanation
Indices: 386016--386056 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
386006 GGCAGTAGCT
386016 AACCTT-CGATTGTATCGATAC
1 AACCTTGCGATTGTATCGATAC
*
386037 AACCTTGTGATTGTATCGAT
1 AACCTTGCGATTGTATCGAT
386057 GCATGTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.37
Consensus pattern (22 bp):
AACCTTGCGATTGTATCGATAC
Found at i:399379 original size:20 final size:19
Alignment explanation
Indices: 399354--399446 Score: 73
Period size: 20 Copynumber: 4.7 Consensus size: 19
399344 CTGCCAGTTT
***
399354 CATGTATCGATACAATTGTG
1 CATGTATCGATACAA-TAAA
399374 CATGTATCGATACAATAAA
1 CATGTATCGATACAATAAA
399393 CATGTATCGATACAA-AGCATA
1 CATGTATCGATACAATA--A-A
* *
399414 -ATGTATCGATACATCTAGA
1 CATGTATCGATACA-ATAAA
*
399433 TATGTATCGATACA
1 CATGTATCGATACA
399447 TACAAGGGTT
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
18 1 0.02
19 17 0.27
20 42 0.68
21 1 0.02
22 1 0.02
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATAAA
Found at i:399447 original size:20 final size:18
Alignment explanation
Indices: 399375--399448 Score: 76
Period size: 20 Copynumber: 3.8 Consensus size: 18
399365 ACAATTGTGC
* *
399375 ATGTATCGATACAATAAAC
1 ATGTATCGATAC-ATAGAT
*
399394 ATGTATCGATACAAAGCAT
1 ATGTATCGATACATAG-AT
399413 AATGTATCGATACATCTAGAT
1 -ATGTATCGATACA--TAGAT
399434 ATGTATCGATACATA
1 ATGTATCGATACATA
399449 CAAGGGTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
18 4 0.09
19 13 0.28
20 26 0.55
21 2 0.04
22 2 0.04
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.30
Consensus pattern (18 bp):
ATGTATCGATACATAGAT
Found at i:400019 original size:77 final size:79
Alignment explanation
Indices: 399924--400068 Score: 233
Period size: 79 Copynumber: 1.9 Consensus size: 79
399914 ATTGGAAAAG
* *
399924 TTCAAATTTCAAAGTTTCATTTTTCT-CCCCTT-ATAAAATAATTATA-GCTCTCATTTTTAAAA
1 TTCAAATATCAAAATTTCATTTTTCTCCCCCTTGATAAAATAATTA-AGGCTCTCATTTTTAAAA
399986 AATTAAGGCTTTCGT
65 AATTAAGGCTTTCGT
*
400001 TTCAAATATCAAAATTTCATTTTTCTCCCCCTTGATAAAATAATTAAGGCTCTCGTTTTTAAAAA
1 TTCAAATATCAAAATTTCATTTTTCTCCCCCTTGATAAAATAATTAAGGCTCTCATTTTTAAAAA
400066 ATT
66 ATT
400069 TTCTCCTCCT
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
77 24 0.39
78 7 0.11
79 31 0.50
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (79 bp):
TTCAAATATCAAAATTTCATTTTTCTCCCCCTTGATAAAATAATTAAGGCTCTCATTTTTAAAAA
ATTAAGGCTTTCGT
Found at i:400458 original size:33 final size:33
Alignment explanation
Indices: 400397--400459 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
400387 AAGTGCACTA
* * *
400397 AAGTGCTCATCCATGCGTTGCGAGAGTGAAGTG
1 AAGTGCTCATCCATGCGCTGCAAAAGTGAAGTG
* *
400430 AAGTGCTCATTCATGTGCTGCAAAAGTGAA
1 AAGTGCTCATCCATGCGCTGCAAAAGTGAA
400460 ATGATCAACT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (33 bp):
AAGTGCTCATCCATGCGCTGCAAAAGTGAAGTG
Found at i:402091 original size:17 final size:17
Alignment explanation
Indices: 402069--402103 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
402059 AATATGGCAA
402069 AATTAGTATCGAACCTT
1 AATTAGTATCGAACCTT
402086 AATTAGTATCGAACCTT
1 AATTAGTATCGAACCTT
402103 A
1 A
402104 CTCTATGATC
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:0.37, C:0.17, G:0.11, T:0.34
Consensus pattern (17 bp):
AATTAGTATCGAACCTT
Found at i:408095 original size:19 final size:20
Alignment explanation
Indices: 408058--408095 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
408048 TCCCGTTGCT
408058 ATGTATCGATACAATTCATA
1 ATGTATCGATACAATTCATA
*
408078 ATGTATTGATAC-ATTCAT
1 ATGTATCGATACAATTCAT
408096 TTGAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACAATTCATA
Found at i:408172 original size:20 final size:19
Alignment explanation
Indices: 408130--408183 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
408120 GTTTGAAGGA
408130 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATTCA-C
408150 ATGTATCGATACAATGTGC-C
1 ATGTATCGATACAAT-T-CAC
*
408170 ATGTATCAATACAA
1 ATGTATCGATACAA
408184 ACAGTGGTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 29 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (19 bp):
ATGTATCGATACAATTCAC
Found at i:408256 original size:19 final size:19
Alignment explanation
Indices: 408212--408267 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
408202 CTGCCAGTTT
**
408212 CATGTATCAATACAATTGTG
1 CATGTATCAATACAA-TGAA
*
408232 CATGTATCTATACAATGAA
1 CATGTATCAATACAATGAA
*
408251 CATGTATCGATACAATG
1 CATGTATCAATACAATG
408268 TATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (19 bp):
CATGTATCAATACAATGAA
Found at i:408270 original size:13 final size:13
Alignment explanation
Indices: 408252--408278 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
408242 TACAATGAAC
408252 ATGTATCGATACA
1 ATGTATCGATACA
408265 ATGTATCGATACA
1 ATGTATCGATACA
408278 A
1 A
408279 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:409636 original size:23 final size:22
Alignment explanation
Indices: 409588--409636 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
409578 CCATCAAATT
* * * *
409588 ATTTTTCCCAAAATTTTCCAAT
1 ATTTTTCCAAAAAGTTTACAAA
409610 ATTTTTCTCAAAAAGTTTACAAA
1 ATTTTTC-CAAAAAGTTTACAAA
409633 ATTT
1 ATTT
409637 CATTTTCAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.37, C:0.16, G:0.02, T:0.45
Consensus pattern (22 bp):
ATTTTTCCAAAAAGTTTACAAA
Found at i:410230 original size:89 final size:90
Alignment explanation
Indices: 410125--410327 Score: 258
Period size: 89 Copynumber: 2.3 Consensus size: 90
410115 AATTTTCAAT
410125 TTTGGGGAAACTCCATCTCC-ACTATTCCAAAGGGATACTT-TAACC-CCAATCTTAAAAAAATT
1 TTTGGGGAAACTCCATCTCCTACTATTCCAAAGGGATA-TTCTAACCTCCAA-CTTAAAAAAATT
* *
410187 CAAATTTTTTCTTTTCAT-AATTTTA-TC
64 CAAA-TTTTTC-CTTCATAAATTTCATTC
* * * *
410214 TTTGGGGAAACTCCATC-CCTACTATTCTAAAGGGATATTCTAACCTCGAACTTCAAAAAATTTA
1 TTTGGGGAAACTCCATCTCCTACTATTCCAAAGGGATATTCTAACCTCCAACTTAAAAAAATTCA
410278 AATTTTTCCTTCATACAATTTCATTC
66 AATTTTTCCTTCATA-AATTTCATTC
410304 TTTGGGGAAACTCCAT-TCCTACTA
1 TTTGGGGAAACTCCATCTCCTACTA
410328 CTCTGAGAGG
Statistics
Matches: 101, Mismatches: 6, Indels: 13
0.84 0.05 0.11
Matches are distributed among these distances:
87 5 0.05
88 10 0.10
89 58 0.57
90 28 0.28
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.37
Consensus pattern (90 bp):
TTTGGGGAAACTCCATCTCCTACTATTCCAAAGGGATATTCTAACCTCCAACTTAAAAAAATTCA
AATTTTTCCTTCATAAATTTCATTC
Found at i:422430 original size:13 final size:13
Alignment explanation
Indices: 422412--422436 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
422402 CATAAAGTGT
422412 TGTATCGATACAA
1 TGTATCGATACAA
422425 TGTATCGATACA
1 TGTATCGATACA
422437 TTTTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:422517 original size:13 final size:13
Alignment explanation
Indices: 422499--422523 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
422489 ATCACTTAAA
422499 TGTATCGATACAT
1 TGTATCGATACAT
422512 TGTATCGATACA
1 TGTATCGATACA
422524 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:423832 original size:5 final size:5
Alignment explanation
Indices: 423815--423865 Score: 72
Period size: 5 Copynumber: 10.8 Consensus size: 5
423805 GTAAACACAA
*
423815 AAAAC AAAA- AAAAC AAAA- AAAAC AAAAA AAAAC AAAAC AAAAC AAAA-
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC
423862 AAAA
1 AAAA
423866 AAGAAGAAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
4 12 0.29
5 30 0.71
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:423833 original size:10 final size:10
Alignment explanation
Indices: 423813--423884 Score: 87
Period size: 10 Copynumber: 7.4 Consensus size: 10
423803 AAGTAAACAC
423813 AAAAAAC-AA
1 AAAAAACAAA
423822 AAAAAAC-AA
1 AAAAAACAAA
423831 AAAAAACAAA
1 AAAAAACAAA
423841 AAAAAACAAA
1 AAAAAACAAA
*
423851 ACAAAACAAA
1 AAAAAACAAA
423861 AAAAAA-AGAA
1 AAAAAACA-AA
* *
423871 GAAAGACAAA
1 AAAAAACAAA
423881 AAAA
1 AAAA
423885 GGTGCAAAGT
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
9 17 0.31
10 37 0.67
11 1 0.02
ACGTcount: A:0.86, C:0.10, G:0.04, T:0.00
Consensus pattern (10 bp):
AAAAAACAAA
Found at i:423862 original size:19 final size:18
Alignment explanation
Indices: 423807--423884 Score: 95
Period size: 19 Copynumber: 4.1 Consensus size: 18
423797 AATCAAAAGT
*
423807 AAACACAAAAAACAAAAA
1 AAACAAAAAAAACAAAAA
423825 AAACAAAAAAAACAAAAAA
1 AAACAAAAAAAAC-AAAAA
423844 AAACAAAACAAAACAAAAA
1 AAACAAAA-AAAACAAAAA
423863 AAA-AAGAAGAAAGACAAAAA
1 AAACAA-AA-AAA-ACAAAAA
423883 AA
1 AA
423885 GGTGCAAAGT
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
18 14 0.26
19 26 0.48
20 14 0.26
ACGTcount: A:0.85, C:0.12, G:0.04, T:0.00
Consensus pattern (18 bp):
AAACAAAAAAAACAAAAA
Found at i:423884 original size:1 final size:1
Alignment explanation
Indices: 423813--423867 Score: 56
Period size: 1 Copynumber: 55.0 Consensus size: 1
423803 AAGTAAACAC
* * * * * *
423813 AAAAAACAAAAAAAACAAAAAAAACAAAAAAAAACAAAACAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
423868 GAAGAAAGAC
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:423885 original size:10 final size:9
Alignment explanation
Indices: 423807--423884 Score: 95
Period size: 9 Copynumber: 8.2 Consensus size: 9
423797 AATCAAAAGT
*
423807 AAACACAAA
1 AAACAAAAA
423816 AAACAAAAA
1 AAACAAAAA
423825 AAACAAAAA
1 AAACAAAAA
423834 AAACAAAAAA
1 AAAC-AAAAA
423844 AAACAAAACA
1 AAACAAAA-A
423854 AAACAAAAA
1 AAACAAAAA
423863 AAA-AAGAAGA
1 AAACAA-AA-A
423873 AAGACAAAAA
1 AA-ACAAAAA
423883 AA
1 AA
423885 GGTGCAAAGT
Statistics
Matches: 62, Mismatches: 1, Indels: 11
0.84 0.01 0.15
Matches are distributed among these distances:
8 2 0.03
9 31 0.50
10 24 0.39
11 3 0.05
12 2 0.03
ACGTcount: A:0.85, C:0.12, G:0.04, T:0.00
Consensus pattern (9 bp):
AAACAAAAA
Found at i:425113 original size:31 final size:31
Alignment explanation
Indices: 425072--425371 Score: 202
Period size: 31 Copynumber: 9.9 Consensus size: 31
425062 CTTCAAATAC
* *
425072 CTTCTTAAAGTCCATGACTCCGTGGCACCTT
1 CTTCTCAAAGTCCACGACTCCGTGGCACCTT
*
425103 CTTCTCAAAGTCCACGACTCAGTGGCATCCTT
1 CTTCTCAAAGTCCACGACTCCGTGGCA-CCTT
* * *
425135 -TTCTTCAAAGTCCACGGCTCAGTGGCA-ATCT
1 CTTC-TCAAAGTCCACGACTCCGTGGCACCT-T
*
425166 CTGCTCAAAGTCCACGACTCCGTGGCACCTT
1 CTTCTCAAAGTCCACGACTCCGTGGCACCTT
* * *
425197 CCTT-TCAAAGCCCACAACTTCGTGGCACTCGTT
1 -CTTCTCAAAGTCCACGACTCCGTGGCAC-C-TT
* * *
425230 -TTCCTTCTAAGTCCATGACTCCGCGGCACCTT
1 CTT-C-TCAAAGTCCACGACTCCGTGGCACCTT
* * *
425262 CTTTTCAAAGCCCACAACTCCGTGGCACC--
1 CTTCTCAAAGTCCACGACTCCGTGGCACCTT
* *
425291 CTT-T-TAAGTCCACAACTCCGTGGCACC--
1 CTTCTCAAAGTCCACGACTCCGTGGCACCTT
* *
425318 CGTT-T--AAGCCCACAACTCCGTGGCACC--
1 C-TTCTCAAAGTCCACGACTCCGTGGCACCTT
* *
425345 CTT-T-TAAGTCCACGACTCTGTGGCACC
1 CTTCTCAAAGTCCACGACTCCGTGGCACC
425372 CTTTTTTCCT
Statistics
Matches: 224, Mismatches: 31, Indels: 32
0.78 0.11 0.11
Matches are distributed among these distances:
26 3 0.01
27 63 0.28
28 4 0.02
29 3 0.01
30 1 0.00
31 93 0.42
32 34 0.15
33 5 0.02
34 18 0.08
ACGTcount: A:0.21, C:0.36, G:0.17, T:0.27
Consensus pattern (31 bp):
CTTCTCAAAGTCCACGACTCCGTGGCACCTT
Found at i:425304 original size:27 final size:27
Alignment explanation
Indices: 425232--425376 Score: 173
Period size: 27 Copynumber: 5.2 Consensus size: 27
425222 CACTCGTTTT
* ** *
425232 CCTTCTAAGTCCATGACTCCGCGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
*
425259 CTTCTTTTCAAAGCCCACAACTCCGTGGCAC
1 C--CTTTT--AAGTCCACAACTCCGTGGCAC
425290 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
* *
425317 CCGTTTAAGCCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
* *
425344 CCTTTTAAGTCCACGACTCTGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
425371 CCTTTT
1 CCTTTT
425377 TTCCTTTAAA
Statistics
Matches: 102, Mismatches: 12, Indels: 8
0.84 0.10 0.07
Matches are distributed among these distances:
27 75 0.74
29 9 0.09
31 18 0.18
ACGTcount: A:0.20, C:0.38, G:0.16, T:0.26
Consensus pattern (27 bp):
CCTTTTAAGTCCACAACTCCGTGGCAC
Found at i:425427 original size:33 final size:32
Alignment explanation
Indices: 425344--425438 Score: 93
Period size: 33 Copynumber: 2.8 Consensus size: 32
425334 TCCGTGGCAC
* *
425344 CCTTTTAAGTCCACGACTCTGTGGCACCCTTTTTT
1 CCTTTTAAGTCCACAACTC-GTGGCA--CTCTTTT
*
425379 CCTTTAAAG-CGCACAACTACGTGGCACTCTTTT
1 CCTTTTAAGTC-CACAACT-CGTGGCACTCTTTT
*
425412 CCTTTTAAGTCCACAAGTTCGTGGCAC
1 CCTTTTAAGTCCACAA-CTCGTGGCAC
425439 CTTCTTCTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
33 27 0.53
34 3 0.06
35 20 0.39
36 1 0.02
ACGTcount: A:0.20, C:0.31, G:0.16, T:0.34
Consensus pattern (32 bp):
CCTTTTAAGTCCACAACTCGTGGCACTCTTTT
Found at i:425468 original size:32 final size:31
Alignment explanation
Indices: 425442--425549 Score: 164
Period size: 33 Copynumber: 3.4 Consensus size: 31
425432 GTGGCACCTT
*
425442 CTTCTAAAGCCCACACAAGTCGGTGGCAACC
1 CTTCTAAAGCCCACACAAGTCGATGGCAACC
425473 CTTCTCAAAGCCCACACAAGTCGATGGCAACC
1 CTTCT-AAAGCCCACACAAGTCGATGGCAACC
*
425505 ATTCTTTAAAGCCCACACAAGTCGATGGCAACC
1 CTTC--TAAAGCCCACACAAGTCGATGGCAACC
425538 CTTCT-AAGCCCA
1 CTTCTAAAGCCCA
425550 ATATAGCTGG
Statistics
Matches: 71, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
30 7 0.10
31 6 0.08
32 28 0.39
33 29 0.41
34 1 0.01
ACGTcount: A:0.31, C:0.35, G:0.16, T:0.19
Consensus pattern (31 bp):
CTTCTAAAGCCCACACAAGTCGATGGCAACC
Found at i:425515 original size:65 final size:62
Alignment explanation
Indices: 425423--425549 Score: 186
Period size: 65 Copynumber: 2.0 Consensus size: 62
425413 CTTTTAAGTC
*
425423 CACAAGTTCGTGGCACCTTCTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCAAAGCCCA
1 CACAAGTTCGTGGCACCTTCTTCTAAAGCCCACACAAGTCGATGGCAACCCTTCT--AAGCCCA
425487 CACAAG-TCGATGGCAACCATTCTT-TAAAGCCCACACAAGTCGATGGCAACCCTTCTAAGCCCA
1 CACAAGTTCG-TGGC-ACC-TTCTTCTAAAGCCCACACAAGTCGATGGCAACCCTTCTAAGCCCA
425550 ATATAGCTGG
Statistics
Matches: 59, Mismatches: 1, Indels: 7
0.88 0.01 0.10
Matches are distributed among these distances:
63 10 0.17
64 10 0.17
65 34 0.58
66 5 0.08
ACGTcount: A:0.29, C:0.35, G:0.17, T:0.20
Consensus pattern (62 bp):
CACAAGTTCGTGGCACCTTCTTCTAAAGCCCACACAAGTCGATGGCAACCCTTCTAAGCCCA
Found at i:425521 original size:33 final size:33
Alignment explanation
Indices: 425423--425542 Score: 167
Period size: 32 Copynumber: 3.7 Consensus size: 33
425413 CTTTTAAGTC
425423 CACAAGTTCG-TGGC-A-CCTTCTTCTAAAGCCCA
1 CACAAG-TCGATGGCAACCCTTCTT-TAAAGCCCA
* *
425455 CACAAGTCGGTGGCAACCCTTC-TCAAAGCCCA
1 CACAAGTCGATGGCAACCCTTCTTTAAAGCCCA
*
425487 CACAAGTCGATGGCAACCATTCTTTAAAGCCCA
1 CACAAGTCGATGGCAACCCTTCTTTAAAGCCCA
425520 CACAAGTCGATGGCAACCCTTCT
1 CACAAGTCGATGGCAACCCTTCT
425543 AAGCCCAATA
Statistics
Matches: 79, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
31 3 0.04
32 38 0.48
33 33 0.42
34 5 0.06
ACGTcount: A:0.28, C:0.34, G:0.17, T:0.21
Consensus pattern (33 bp):
CACAAGTCGATGGCAACCCTTCTTTAAAGCCCA
Found at i:425600 original size:49 final size:49
Alignment explanation
Indices: 425542--426434 Score: 1155
Period size: 49 Copynumber: 18.7 Consensus size: 49
425532 GCAACCCTTC
* * ** *
425542 TAAGCCCAATATAGCTGGCCTTGAATCAATATATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
425591 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
425634 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC---CTTCATCTT
425686 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
425729 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * *
425778 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTAGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
425827 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
425876 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
425919 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
425968 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
426011 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * * *
426060 TAAGTCCAATATAGTTGGCCTTGAATTAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
426109 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * * *
426158 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTAGAACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
426207 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
426256 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCACCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
426304 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
426347 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
*
426399 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
426435 ACATCCTTTT
Statistics
Matches: 745, Mismatches: 63, Indels: 69
0.85 0.07 0.08
Matches are distributed among these distances:
43 197 0.26
45 5 0.01
47 3 0.00
48 45 0.06
49 417 0.56
50 2 0.00
52 76 0.10
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (49 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
Found at i:425976 original size:92 final size:92
Alignment explanation
Indices: 425824--426498 Score: 750
Period size: 92 Copynumber: 7.1 Consensus size: 92
425814 GCACCTTTAT
* *
425824 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATA
425889 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* * * *
425916 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATA
425981 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* * *
426008 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATA
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATA
* * *
426073 GTTGGCCTTGAATTAGCATATTGGCACC
66 GCTGGCCTTGAATCAGCACATTGGCA-C
* * *
426101 TTTATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCA
1 -----CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCA
* * *
426166 ATATAGCTGGCCTTGAATCAGCATATTAGAACCTTTAT
61 ATATAGCTGGCCTTGAATCAGCACATT-G--GC---AC
* *
426204 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATA
426269 GCTGGCCTTGAATCAGCACATTGGCACCTCAC
66 GCTGGCCTTGAATCAGCACATTGG-----CAC
426301 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATA
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATA
*
426360 GCTGGCCTTGAATCAGCATATTGGCACCTTTTCC
66 GCTGGCCTTGAATCAGCACATTGGCA-------C
* * *
426394 ATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCATCTTTAAGC
1 --CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CC----T-TCATCTTTAAGT
* * * * * *
426459 CCAATATCGTTGGCCGTGAATCAACATATTGGCAT
58 CCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
426494 CTTTA
1 CTTTA
426499 TCACTTTTCT
Statistics
Matches: 510, Mismatches: 35, Indels: 70
0.83 0.06 0.11
Matches are distributed among these distances:
86 2 0.00
91 38 0.07
92 175 0.34
93 3 0.01
95 40 0.08
97 43 0.08
98 167 0.33
99 1 0.00
100 1 0.00
101 1 0.00
104 1 0.00
105 1 0.00
107 37 0.07
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.32
Consensus pattern (92 bp):
CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATA
GCTGGCCTTGAATCAGCACATTGGCAC
Found at i:426473 original size:55 final size:52
Alignment explanation
Indices: 426344--426481 Score: 177
Period size: 52 Copynumber: 2.6 Consensus size: 52
426334 ACATTGGCAC
* *
426344 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACACCTTTTCCAT
* *
426396 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACA-CC-TTTTC-CAT
* * * *
426451 CTTTAAGCCCAATATCGTTGGCCGTGAATCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCA
426482 ACATATTGGC
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
52 38 0.52
53 2 0.03
54 5 0.07
55 28 0.38
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.35
Consensus pattern (52 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACACCTTTTCCAT
Found at i:426555 original size:67 final size:68
Alignment explanation
Indices: 426447--426573 Score: 193
Period size: 67 Copynumber: 1.9 Consensus size: 68
426437 ATCCTTTTTC
* *
426447 TCATCTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTTATCA-CTTTTCTCA
1 TCATCTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCACCTTCATCATCTTTTCTCA
426511 TCT
66 TCT
* * * *
426514 TCATCTTTAAGTCCAATATTGTTGGCCTTGAATCAGCATATTGGCACCTTCATCATCTTT
1 TCATCTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCACCTTCATCATCTTT
426574 AAAACCCAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
67 49 0.92
68 4 0.08
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (68 bp):
TCATCTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCACCTTCATCATCTTTTCTCA
TCT
Found at i:427403 original size:13 final size:13
Alignment explanation
Indices: 427385--427409 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
427375 CATAAAGTGT
427385 TGTATCGATACAA
1 TGTATCGATACAA
427398 TGTATCGATACA
1 TGTATCGATACA
427410 TATTTTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:427491 original size:13 final size:13
Alignment explanation
Indices: 427473--427497 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
427463 ATCACTTAAA
427473 TGTATCGATACAT
1 TGTATCGATACAT
427486 TGTATCGATACA
1 TGTATCGATACA
427498 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:436066 original size:13 final size:13
Alignment explanation
Indices: 436044--436080 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
436034 TATGCATGAA
436044 AAAAAGAAAAAATT
1 AAAAA-AAAAAATT
436058 -AAAAAAAAAATT
1 AAAAAAAAAAATT
436070 AAAAAAAAAAA
1 AAAAAAAAAAA
436081 GAAAAATCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.86, C:0.00, G:0.03, T:0.11
Consensus pattern (13 bp):
AAAAAAAAAAATT
Found at i:436067 original size:12 final size:12
Alignment explanation
Indices: 436045--436079 Score: 61
Period size: 12 Copynumber: 2.8 Consensus size: 12
436035 ATGCATGAAA
436045 AAAAGAAAAAATT
1 AAAA-AAAAAATT
436058 AAAAAAAAAATT
1 AAAAAAAAAATT
436070 AAAAAAAAAA
1 AAAAAAAAAA
436080 AGAAAAATCG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 18 0.82
13 4 0.18
ACGTcount: A:0.86, C:0.00, G:0.03, T:0.11
Consensus pattern (12 bp):
AAAAAAAAAATT
Found at i:436085 original size:12 final size:12
Alignment explanation
Indices: 436044--436086 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
436034 TATGCATGAA
436044 AAAAAGAAAAAATT
1 AAAAA-AAAAAA-T
*
436058 AAAAAAAAAATT
1 AAAAAAAAAAAT
*
436070 AAAAAAAAAAAG
1 AAAAAAAAAAAT
436082 AAAAA
1 AAAAA
436087 TCGAATGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 16 0.62
13 5 0.19
14 5 0.19
ACGTcount: A:0.86, C:0.00, G:0.05, T:0.09
Consensus pattern (12 bp):
AAAAAAAAAAAT
Found at i:437729 original size:42 final size:42
Alignment explanation
Indices: 437670--438572 Score: 603
Period size: 42 Copynumber: 21.4 Consensus size: 42
437660 CTTTAATCTA
** * *
437670 CCTGTCGATTTTGACCTTGGAGACTACCTCACCTAAAGTCTG
1 CCTGTCGGCTTTGACCTTGGAGACTTCCTCACCTCAAGTCTG
* * *
437712 CCTGTCGGCTTTGACCTTGGAGACTTTCTTACC-CTTAGTCTG
1 CCTGTCGGCTTTGACCTTGGAGACTTCCTCACCTC-AAGTCTG
* * ** * * * *
437754 TCTATTAGCTTTGACCTTAGAAACTGCCTCATCTCAAGTCTG
1 CCTGTCGGCTTTGACCTTGGAGACTTCCTCACCTCAAGTCTG
* * ** *
437796 TCAGTCAACTTTGGCCTTGGAGACATTCCT-ACCTTC-AGTCTG
1 CCTGTCGGCTTTGACCTTGGAGAC-TTCCTCACC-TCAAGTCTG
* * * *
437838 CTTGTCGGCTTTGACCCTAGAGACTT-TTCTACCTTC-AGTCTG
1 CCTGTCGGCTTTGACCTTGGAGACTTCCTC-ACC-TCAAGTCTG
* * * * *
437880 CCTATAGACTTTGACCTTGGAGACTGCCTCACCTTAAGTCTG
1 CCTGTCGGCTTTGACCTTGGAGACTTCCTCACCTCAAGTCTG
* * * *
437922 CTTGTAGGCTTTGACCTTGGAGACTTTCTTACCCTC-AGTCTG
1 CCTGTCGGCTTTGACCTTGGAGACTTCCTCA-CCTCAAGTCTG
* * ** * * * *
437964 CCTATCGGCTTTGACCCTAAAGACTACCTCACTTCAAGTTTA
1 CCTGTCGGCTTTGACCTTGGAGACTTCCTCACCTCAAGTCTG
* * * *
438006 CCTATCGGTTTTGACCCTGAAGACTTTCCT-ACCTTC-AGTCTG
1 CCTGTCGGCTTTGACCTTGGAGAC-TTCCTCACC-TCAAGTCTG
* *
438048 CCTGTCGGCTTTGACCTTGGAGACTACCCCACCTCAAGTCTG
1 CCTGTCGGCTTTGACCTTGGAGACTTCCTCACCTCAAGTCTG
* * * * *
438090 CTTGTCAGCTTTGACCTTGGAGACTTTCTTACCCTC-AGTATG
1 CCTGTCGGCTTTGACCTTGGAGACTTCCTCA-CCTCAAGTCTG
* * * * *
438132 CTTGTCGGCTTTGACCCTAGAGACTGCCCCACCTCAAGTCTG
1 CCTGTCGGCTTTGACCTTGGAGACTTCCTCACCTCAAGTCTG
* * * * * * * * *
438174 CCTGTTGACTTTCACGTTGGAAACTTTCTTACC-CTTAGTCTA
1 CCTGTCGGCTTTGACCTTGGAGACTTCCTCACCTC-AAGTCTG
* * * * * *
438216 CCTATCGGCTTTGACCCTAGAGACTGCTTTACCTCAAGTCTG
1 CCTGTCGGCTTTGACCTTGGAGACTTCCTCACCTCAAGTCTG
* * * *
438258 CTTGTTGGCTTTGACCTTGGAGACTTTCTTACCCTCAAGTCTG
1 CCTGTCGGCTTTGACCTTGGAGACTTCCTCA-CCTCAAGTCTG
* * * * *
438301 CCTGTCGGCTTTGACCCTAGAGACTTTCTTACC-CTTAGTCTG
1 CCTGTCGGCTTTGACCTTGGAGACTTCCTCACCTC-AAGTCTG
* * * *
438343 CCTATCGACTTTGACGC-TAGAGACTACCTCACCTCAAGTCTG
1 CCTGTCGGCTTTGAC-CTTGGAGACTTCCTCACCTCAAGTCTG
* * * *
438385 CCTGTCGACTTTGACCTTAGAGACTTTCCT-ATCTTC-AGTCTA
1 CCTGTCGGCTTTGACCTTGGAGAC-TTCCTCA-CCTCAAGTCTG
* * *
438427 CTTGTCGGCTTTGACCTTGGAGACTACCACACCTCAAGTCTG
1 CCTGTCGGCTTTGACCTTGGAGACTTCCTCACCTCAAGTCTG
* * * * * *
438469 CCTATCAGCTTTGACCTTAGAAAGTTCCTTACCCTCAAGTCTG
1 CCTGTCGGCTTTGACCTTGGAGACTTCCTCA-CCTCAAGTCTG
* * * * *
438512 CCTATCAGCTTTGACCCTAGAGACTTTCAT-ACCCTCAAGTCTG
1 CCTGTCGGCTTTGACCTTGGAGAC-TTCCTCA-CCTCAAGTCTG
*
438555 CCTGTTGGCTTTGACCTT
1 CCTGTCGGCTTTGACCTT
438573 ATAAAGTTTT
Statistics
Matches: 667, Mismatches: 165, Indels: 57
0.75 0.19 0.06
Matches are distributed among these distances:
40 1 0.00
41 24 0.04
42 509 0.76
43 129 0.19
44 4 0.01
ACGTcount: A:0.18, C:0.30, G:0.18, T:0.34
Consensus pattern (42 bp):
CCTGTCGGCTTTGACCTTGGAGACTTCCTCACCTCAAGTCTG
Found at i:438023 original size:168 final size:168
Alignment explanation
Indices: 437816--438573 Score: 734
Period size: 168 Copynumber: 4.5 Consensus size: 168
437806 TTGGCCTTGG
* *
437816 AGACATTCCT-ACCTTC-AGTCTGCTTGTCGGCTTTGACCCTAGAGACTTTTCTACCTTCAGTCT
1 AGAC-TTCCTCACC-TCAAGTCTGCCTATCGGCTTTGACCCTAGAGAC-TTTCTACCTTCAGTCT
* * * * *
437879 GCCTATAGACTTTGACCTTGGAGACTGCCTCACCTTAAGTCTGCTTGTAGGCTTTGACCTTGGAG
63 GCCTGTCGGCTTTGACCTTAGAGACTGCCTCACCTCAAGTCTGCTTGTAGGCTTTGACCTTGGAG
437944 ACTTTCTTACCCTC-AGTCTGCCTATCGGCTTTGACCCTAA
128 ACTTTCTTACCCTCAAGTCTGCCTATCGGCTTTGACCCTAA
* * * * *
437984 AGACTACCTCACTTCAAGTTTACCTATCGGTTTTGACCCT-GAAGACTTTCCTACCTTCAGTCTG
1 AGACTTCCTCACCTCAAGTCTGCCTATCGGCTTTGACCCTAG-AGACTTT-CTACCTTCAGTCTG
* * *
438048 CCTGTCGGCTTTGACCTTGGAGACTACCCCACCTCAAGTCTGCTTGTCA-GCTTTGACCTTGGAG
64 CCTGTCGGCTTTGACCTTAGAGACTGCCTCACCTCAAGTCTGCTTGT-AGGCTTTGACCTTGGAG
* * * *
438112 ACTTTCTTACCCTC-AGTATGCTTGTCGGCTTTGACCCTAG
128 ACTTTCTTACCCTCAAGTCTGCCTATCGGCTTTGACCCTAA
* * * * * * ** * * *
438152 AGACTGCCCCACCTCAAGTCTGCCTGTTGACTTTCACGTTGGAAACTTTCTTACCCTT-AGTCTA
1 AGACTTCCTCACCTCAAGTCTGCCTATCGGCTTTGACCCTAGAGACTTTC-TA-CCTTCAGTCTG
* * * * *
438216 CCTATCGGCTTTGACCCTAGAGACTGCTTTACCTCAAGTCTGCTTGTTGGCTTTGACCTTGGAGA
64 CCTGTCGGCTTTGACCTTAGAGACTGCCTCACCTCAAGTCTGCTTGTAGGCTTTGACCTTGGAGA
* *
438281 CTTTCTTACCCTCAAGTCTGCCTGTCGGCTTTGACCCTAG
129 CTTTCTTACCCTCAAGTCTGCCTATCGGCTTTGACCCTAA
* * * * * **
438321 AGACTTTCTTACC-CTTAGTCTGCCTATCGACTTTGACGCTAGAGACTACCTCACC-TCAAGTCT
1 AGACTTCCTCACCTC-AAGTCTGCCTATCGGCTTTGACCCTAGAGACTTTCT-ACCTTC-AGTCT
* * * * *
438384 GCCTGTCGACTTTGACCTTAGAGACTTTCCT-ATCTTC-AGTCTACTTGTCGGCTTTGACCTTGG
63 GCCTGTCGGCTTTGACCTTAGAGAC-TGCCTCA-CCTCAAGTCTGCTTGTAGGCTTTGACCTTGG
* * * *
438447 AGAC-TAC-CACACCTCAAGTCTGCCTATCAGCTTTGACCTTAGA
126 AGACTTTCTTAC-CCTCAAGTCTGCCTATCGGCTTTGACCCTA-A
* * * *
438490 A-AGTTCCTTACCCTCAAGTCTGCCTATCAGCTTTGACCCTAGAGACTTTCATACCCTCAAGTCT
1 AGACTTCCTCA-CCTCAAGTCTGCCTATCGGCTTTGACCCTAGAGACTTTC-TACCTTC-AGTCT
*
438554 GCCTGTTGGCTTTGACCTTA
63 GCCTGTCGGCTTTGACCTTA
438574 TAAAGTTTTA
Statistics
Matches: 489, Mismatches: 79, Indels: 42
0.80 0.13 0.07
Matches are distributed among these distances:
167 14 0.03
168 285 0.58
169 156 0.32
170 34 0.07
ACGTcount: A:0.19, C:0.30, G:0.18, T:0.34
Consensus pattern (168 bp):
AGACTTCCTCACCTCAAGTCTGCCTATCGGCTTTGACCCTAGAGACTTTCTACCTTCAGTCTGCC
TGTCGGCTTTGACCTTAGAGACTGCCTCACCTCAAGTCTGCTTGTAGGCTTTGACCTTGGAGACT
TTCTTACCCTCAAGTCTGCCTATCGGCTTTGACCCTAA
Found at i:438378 original size:211 final size:209
Alignment explanation
Indices: 437995--438557 Score: 630
Period size: 211 Copynumber: 2.7 Consensus size: 209
437985 GACTACCTCA
* *
437995 CTTCAAGTTTACCTATCGGTTTTGACCCTGAAGACT-TTCCTACCTTC-AGTCTGCCTGTCGGCT
1 CTTC-AGTCTACCTATCGGCTTTGACCCTG-AGACTCTT--TACC-TCAAGTCTGCCTGTCGGCT
* ** * * *
438058 TTGACCTTGGAGACTACCCCA-CCTCAAGTCTGCTTGTCAGCTTTGACCTTGGAGACTTTCTTAC
61 TTGACCTTGGAGACTTCCTTACCCTCAAGTCTGCCTGTCAGCTTTGACCCTAGAGACTTTCTTAC
* * * * * * *
438122 CCTCAGTATGCTTGTCGGCTTTGACCCTAGAGACTGCCCCACCTCAAGTCTGCCTGTTGACTTTC
126 CCTAAGTCTGCCTATCGACTTTGACCCTAGAGACTACCCCACCTCAAGTCTGCCTGTCGACTTTC
* * *
438187 ACGTTGGAAACTTTCTTACC
191 ACCTTAGAAACTTTCCTA-C
* *
438207 CTT-AGTCTACCTATCGGCTTTGACCCTAGAGACTGCTTTACCTCAAGTCTGCTTGTTGGCTTTG
1 CTTCAGTCTACCTATCGGCTTTGACCCT-GAGACT-CTTTACCTCAAGTCTGCCTGTCGGCTTTG
* *
438271 ACCTTGGAGACTTTCTTACCCTCAAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCTTACCCT
64 ACCTTGGAGACTTCCTTACCCTCAAGTCTGCCTGTCAGCTTTGACCCTAGAGACTTTCTTACCCT
* * * *
438336 TAGTCTGCCTATCGACTTTGACGCTAGAGACTACCTCACCTCAAGTCTGCCTGTCGACTTTGACC
129 AAGTCTGCCTATCGACTTTGACCCTAGAGACTACCCCACCTCAAGTCTGCCTGTCGACTTTCACC
* *
438401 TTAGAGACTTTCCTAT
194 TTAGAAACTTTCCTAC
* * * *** * *
438417 CTTCAGTCTACTTGTCGGCTTTGACCTTGGAGACTACCACACCTCAAGTCTGCCTATCAGCTTTG
1 CTTCAGTCTACCTATCGGCTTTGACCCT-GAGACT-CTTTACCTCAAGTCTGCCTGTCGGCTTTG
* * * * *
438482 ACCTTAGAAAGTTCCTTACCCTCAAGTCTGCCTATCAGCTTTGACCCTAGAGACTTTCATACCCT
64 ACCTTGGAGACTTCCTTACCCTCAAGTCTGCCTGTCAGCTTTGACCCTAGAGACTTTCTTACCCT
438547 CAAGTCTGCCT
129 -AAGTCTGCCT
438558 GTTGGCTTTG
Statistics
Matches: 297, Mismatches: 47, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
209 2 0.01
210 65 0.22
211 216 0.73
212 14 0.05
ACGTcount: A:0.19, C:0.31, G:0.18, T:0.33
Consensus pattern (209 bp):
CTTCAGTCTACCTATCGGCTTTGACCCTGAGACTCTTTACCTCAAGTCTGCCTGTCGGCTTTGAC
CTTGGAGACTTCCTTACCCTCAAGTCTGCCTGTCAGCTTTGACCCTAGAGACTTTCTTACCCTAA
GTCTGCCTATCGACTTTGACCCTAGAGACTACCCCACCTCAAGTCTGCCTGTCGACTTTCACCTT
AGAAACTTTCCTAC
Found at i:450244 original size:12 final size:11
Alignment explanation
Indices: 450222--450297 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
450212 AGAGAAAGAA
*
450222 GAGAGAGGAGG
1 GAGATAGGAGG
450233 GATGATAGGAGG
1 GA-GATAGGAGG
*
450245 AGAGACAGGA--
1 -GAGATAGGAGG
*
450255 GAGATAGTA--
1 GAGATAGGAGG
450264 GAGATAGGAGG
1 GAGATAGGAGG
450275 GATGATAGGAGG
1 GA-GATAGGAGG
*
450287 AGAGACAGGAG
1 -GAGATAGGAG
450298 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:450254 original size:24 final size:24
Alignment explanation
Indices: 450221--450306 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
450211 AAGAGAAAGA
*
450221 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
450245 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
450263 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
450287 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
450307 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:450273 original size:42 final size:42
Alignment explanation
Indices: 450212--450327 Score: 187
Period size: 42 Copynumber: 2.8 Consensus size: 42
450202 TAGCCCTCAA
* *
450212 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
450254 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
450296 AGAGATAATAGAGAGAGGAGGGATGACAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAG
450328 AAGGAGAGAA
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.09
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:456057 original size:13 final size:12
Alignment explanation
Indices: 456036--456095 Score: 54
Period size: 12 Copynumber: 5.0 Consensus size: 12
456026 TTTAGAAAGT
456036 GAAAA-AAAAAA
1 GAAAAGAAAAAA
456047 GAAATAG-AAAAA
1 GAAA-AGAAAAAA
456059 GAAAAGAAAGAAA
1 GAAAAGAAA-AAA
*
456072 G-AAAGAAAAGAT
1 GAAAAGAAAA-AA
*
456084 GAAAATAAAAAA
1 GAAAAGAAAAAA
456096 AAATTTATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
11 7 0.17
12 22 0.55
13 11 0.28
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (12 bp):
GAAAAGAAAAAA
Found at i:456076 original size:17 final size:17
Alignment explanation
Indices: 456029--456082 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
456019 ACCTAGTTTT
* *
456029 AGAAAGTGAAAAAAAAA
1 AGAAAGAGAAAAAGAAA
*
456046 AGAAATAGAAAAAGAAA
1 AGAAAGAGAAAAAGAAA
456063 AGAAAGA-AAGAAAGAAA
1 AGAAAGAGAA-AAAGAAA
456080 AGA
1 AGA
456083 TGAAAATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
16 2 0.06
17 30 0.94
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (17 bp):
AGAAAGAGAAAAAGAAA
Found at i:456087 original size:25 final size:25
Alignment explanation
Indices: 456031--456099 Score: 69
Period size: 24 Copynumber: 2.9 Consensus size: 25
456021 CTAGTTTTAG
456031 AAAG-TGAAAAAAAAAAGAAATAGA
1 AAAGATGAAAAAAAAAAGAAATAGA
456055 AAA-A-GAAAAGAAAGAAAG-AA-AGA
1 AAAGATGAAAA-AAA-AAAGAAATAGA
456078 AAAGATGAAAATAAAAAA-AAAT
1 AAAGATGAAAA-AAAAAAGAAAT
456100 TTATTTATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
23 11 0.30
24 14 0.38
25 12 0.32
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (25 bp):
AAAGATGAAAAAAAAAAGAAATAGA
Found at i:456604 original size:49 final size:49
Alignment explanation
Indices: 456462--456682 Score: 191
Period size: 49 Copynumber: 4.5 Consensus size: 49
456452 GTTAATACAA
* *
456462 AGTCTTTTAAGGTTGGTTTTATACTTTCTATCAAAATCGACCAAAATCG
1 AGTCTTTTAAGGTTAGTTTTGTACTTTCTATCAAAATCGACCAAAATCG
* * * * *
456511 AGTCTTTT-AGTGTTAG-TTTGTGCATTCTATCAAAAACAACCAAAATTG
1 AGTCTTTTAAG-GTTAGTTTTGTACTTTCTATCAAAATCGACCAAAATCG
* * * *
456559 AGTCTTTTAAGGTTAGTTTTGTACTTTTTATCAAAATTGATCAAAATCA
1 AGTCTTTTAAGGTTAGTTTTGTACTTTCTATCAAAATCGACCAAAATCG
* * ** ** * *
456608 AGT-TTTATAGGGTTAGATTTAAACAATCCATCAAAATCGA-CAATAATCA
1 AGTCTTT-TAAGGTTAGTTTTGTACTTTCTATCAAAATCGACCAA-AATCG
*
456657 AGT-TTTTGAATGTTAGTTTTGTACTT
1 AGTCTTTT-AAGGTTAGTTTTGTACTT
456683 CTTGTCAAAA
Statistics
Matches: 134, Mismatches: 32, Indels: 12
0.75 0.18 0.07
Matches are distributed among these distances:
48 48 0.36
49 86 0.64
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (49 bp):
AGTCTTTTAAGGTTAGTTTTGTACTTTCTATCAAAATCGACCAAAATCG
Found at i:458071 original size:13 final size:13
Alignment explanation
Indices: 458053--458109 Score: 51
Period size: 13 Copynumber: 4.0 Consensus size: 13
458043 ACATAAGTGT
458053 TGTATCGATACAA
1 TGTATCGATACAA
*
458066 TGTATCGATAATAA
1 TGTATCGAT-ACAA
458080 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
*
458097 TGTATCGCTACAA
1 TGTATCGATACAA
458110 AGCTACTGCC
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
13 21 0.58
14 3 0.08
17 3 0.08
18 9 0.25
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:458083 original size:31 final size:32
Alignment explanation
Indices: 458036--458108 Score: 130
Period size: 31 Copynumber: 2.3 Consensus size: 32
458026 ACAGTAAATA
458036 TATCGATACATAAGTGTTGTATCGATACAATG
1 TATCGATACATAAGTGTTGTATCGATACAATG
458068 TATCGATA-ATAAGTGTTGTATCGATACAATG
1 TATCGATACATAAGTGTTGTATCGATACAATG
*
458099 TATCGCTACA
1 TATCGATACA
458109 AAGCTACTGC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
31 30 0.77
32 9 0.23
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (32 bp):
TATCGATACATAAGTGTTGTATCGATACAATG
Found at i:458165 original size:13 final size:13
Alignment explanation
Indices: 458147--458174 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
458137 CATTATTCAA
458147 TGTATCGATACAT
1 TGTATCGATACAT
458160 TGTATCGATACAT
1 TGTATCGATACAT
458173 TG
1 TG
458175 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:458169 original size:33 final size:33
Alignment explanation
Indices: 458127--458192 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
458117 GCCAAGGAAA
458127 TGTATCGATACATT-ATTCAATGTATCGATACAT
1 TGTATCGATACATTGA-TCAATGTATCGATACAT
**
458160 TGTATCGATACATTGATCTTTGTATCGATACAT
1 TGTATCGATACATTGATCAATGTATCGATACAT
458193 CTGGGAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (33 bp):
TGTATCGATACATTGATCAATGTATCGATACAT
Found at i:464349 original size:17 final size:17
Alignment explanation
Indices: 464312--464364 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
464302 TAATATTTTG
*
464312 AATTAAAT-ATTAATA-
1 AATTAAATAAATAATAT
464327 AA-TAAATAAATAATAT
1 AATTAAATAAATAATAT
464343 AATTAAAATAAA-AATAT
1 AATT-AAATAAATAATAT
464360 AATTA
1 AATTA
464365 CATTTTTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.15
15 8 0.24
16 3 0.09
17 10 0.30
18 7 0.21
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AATTAAATAAATAATAT
Found at i:464798 original size:9 final size:9
Alignment explanation
Indices: 464784--464824 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
464774 ACGTTATATT
464784 ATATTTAAA
1 ATATTTAAA
*
464793 ATATTTTATA
1 ATA-TTTAAA
464803 ATATTTAAA
1 ATATTTAAA
464812 AT-TTTAAA
1 ATATTTAAA
464820 ATATT
1 ATATT
464825 AATAATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 8 0.29
9 12 0.43
10 8 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
ATATTTAAA
Found at i:464834 original size:33 final size:33
Alignment explanation
Indices: 464792--464877 Score: 102
Period size: 33 Copynumber: 2.5 Consensus size: 33
464782 TTATATTTAA
464792 AATATTTTATAATATTTAAAATTTTAAA-ATATT
1 AATATTTTATAATATTTAAAATTTTAAATAT-TT
* * * *
464825 AATAATTTATATTATATAAAATTTTATATATTT
1 AATATTTTATAATATTTAAAATTTTAAATATTT
464858 ATATATTTATATAATATTTA
1 A-ATATTT-TATAATATTTA
464878 TATTATTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
33 27 0.63
34 7 0.16
35 9 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (33 bp):
AATATTTTATAATATTTAAAATTTTAAATATTT
Found at i:464841 original size:5 final size:5
Alignment explanation
Indices: 464831--464973 Score: 90
Period size: 5 Copynumber: 29.4 Consensus size: 5
464821 TATTAATAAT
* * * *
464831 TTATA TTATA TAAAA TTTTA -TATA TT-TA -TATA TTTATA TAATA TTTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA -TTATA TTATA -TTATA
*
464880 TTAT- TT-T- TTATA TTATA TTATA TTATA TTATA TTTTAA TTAT- TT-T-
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTAT-A TTATA TTATA
* * *
464925 TTATA TTATA TT-TA TTTATA TAATTA TTTTT TTATTA TTATA TTATA
1 TTATA TTATA TTATA -TTATA TTA-TA TTATA TTA-TA TTATA TTATA
464972 TT
1 TT
464974 TAAAATTATC
Statistics
Matches: 108, Mismatches: 16, Indels: 28
0.71 0.11 0.18
Matches are distributed among these distances:
3 7 0.06
4 15 0.14
5 65 0.60
6 21 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTATA
Found at i:464879 original size:17 final size:17
Alignment explanation
Indices: 464793--464975 Score: 60
Period size: 17 Copynumber: 11.4 Consensus size: 17
464783 TATATTTAAA
464793 ATATTT-TATAATATTT
1 ATATTTATATAATATTT
* * *
464809 AAAATTT-TAAAATATTA
1 -ATATTTATATAATATTT
* *
464826 ATAATTTATATTATA-TA
1 AT-ATTTATATAATATTT
*
464843 AAATTT-TAT-ATATTTAT
1 ATATTTATATAATA-TT-T
464860 ATATTTATATAATATTT
1 ATATTTATATAATATTT
464877 ATA-TTAT-T--T-TTT
1 ATATTTATATAATATTT
*
464889 ATA-TTATATTATA-TT
1 ATATTTATATAATATTT
** *
464904 ATA-TTATATTTTAATT
1 ATATTTATATAATATTT
* *
464920 AT-TTTTTATATTATATT
1 ATATTTATATAATAT-TT
464937 -TATTTATATAATTATTT
1 ATATTTATATAA-TATTT
*
464954 -T-TTTAT-TATTATATT
1 ATATTTATATAATAT-TT
464969 ATATTTA
1 ATATTTA
464976 AAATTATCAA
Statistics
Matches: 131, Mismatches: 16, Indels: 38
0.71 0.09 0.21
Matches are distributed among these distances:
12 10 0.08
13 2 0.02
14 6 0.05
15 23 0.18
16 29 0.22
17 45 0.34
18 13 0.10
19 3 0.02
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATATTTATATAATATTT
Found at i:464960 original size:38 final size:37
Alignment explanation
Indices: 464845--464975 Score: 160
Period size: 38 Copynumber: 3.5 Consensus size: 37
464835 ATTATATAAA
* *
464845 ATTTTATATATT-TATATATTTATATAATATTTATATT
1 ATTTTTTATATTATATTTATTTATATAATATTT-TATT
*
464882 ATTTTTTATATTATA-TTATATTATATTATATTTTAATT
1 ATTTTTTATATTATATTTAT-TTATATAATATTTT-ATT
*
464920 ATTTTTTATATTATATTTATTTATATAATTATTTTTTT
1 ATTTTTTATATTATATTTATTTATATAA-TATTTTATT
*
464958 A-TTATTATATTATATTTA
1 ATTTTTTATATTATATTTA
464976 AAATTATCAA
Statistics
Matches: 83, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
37 31 0.37
38 42 0.51
39 10 0.12
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (37 bp):
ATTTTTTATATTATATTTATTTATATAATATTTTATT
Found at i:466809 original size:15 final size:15
Alignment explanation
Indices: 466784--466840 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
466774 TAAATGTGCG
*
466784 ATAAATTTAAAAATT
1 ATAAATATAAAAATT
* *
466799 ATAAAAATAAAATAAT
1 ATAAATATAAAA-ATT
*
466815 ATAAATATAAAATTT
1 ATAAATATAAAAATT
*
466830 TTAAATATAAA
1 ATAAATATAAA
466841 TAATATAACA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
15 21 0.62
16 13 0.38
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
ATAAATATAAAAATT
Found at i:466842 original size:30 final size:31
Alignment explanation
Indices: 466784--466848 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
466774 TAAATGTGCG
*
466784 ATAAATTTAAAAATTATAAAAATAAAATAAT
1 ATAAATATAAAAATTATAAAAATAAAATAAT
* * *
466815 ATAAATATAAAATTTTTAAATAT-AAATAAT
1 ATAAATATAAAAATTATAAAAATAAAATAAT
466845 ATAA
1 ATAA
466849 CATTTATAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 11 0.37
31 19 0.63
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (31 bp):
ATAAATATAAAAATTATAAAAATAAAATAAT
Found at i:466863 original size:23 final size:22
Alignment explanation
Indices: 466810--466870 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
466800 TAAAAATAAA
466810 ATAATATAAAT-ATA-AAATTT
1 ATAATATAAATAATATAAATTT
*
466830 TTAAATATAAATAATATAACATTT
1 AT-AATATAAATAATATAA-ATTT
*
466854 ATAATATAAATATTATA
1 ATAATATAAATAATATA
466871 TTTATATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 1 0.03
21 9 0.26
22 3 0.09
23 16 0.47
24 5 0.15
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
ATAATATAAATAATATAAATTT
Found at i:472208 original size:25 final size:27
Alignment explanation
Indices: 472180--472254 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
472170 CTTGACAAGT
472180 TTAAAAATAGGGTTGGAGTA-C-CCTC
1 TTAAAAATAGGGTTGGAGTATCTCCTC
* *
472205 TTAAAAAAAGGAGTGGGAGTATCTCCTC
1 TTAAAAATAGG-GTTGGAGTATCTCCTC
** *
472233 AGAAGAATAGGGTTGGAGTATC
1 TTAAAAATAGGGTTGGAGTATC
472255 CCGTGAATGA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
25 10 0.25
26 8 0.20
27 11 0.28
28 11 0.28
ACGTcount: A:0.35, C:0.12, G:0.28, T:0.25
Consensus pattern (27 bp):
TTAAAAATAGGGTTGGAGTATCTCCTC
Found at i:474666 original size:52 final size:52
Alignment explanation
Indices: 474583--474722 Score: 183
Period size: 52 Copynumber: 2.7 Consensus size: 52
474573 ATTTAACTAG
* * *
474583 ATGTATCGATACATTGAAGAATGTATCGATACATTTAGT-ACAAAAACTCAGA
1 ATGTATCGATACAATGAAGAATGTATCGATACATTT-GTGACAAAAACCCAAA
* * * *
474635 ATGTATCTATACAATGAAGAATCTATTGATACATTTGTGTCAAAAACCCAAA
1 ATGTATCGATACAATGAAGAATGTATCGATACATTTGTGACAAAAACCCAAA
* *
474687 ATGTATCGATACAATAAAAAATGTATCGATACATTT
1 ATGTATCGATACAATGAAGAATGTATCGATACATTT
474723 TCTTTCCAAA
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
51 2 0.03
52 73 0.97
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.31
Consensus pattern (52 bp):
ATGTATCGATACAATGAAGAATGTATCGATACATTTGTGACAAAAACCCAAA
Found at i:474815 original size:20 final size:20
Alignment explanation
Indices: 474774--474825 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
474764 GATTTCAAGC
*
474774 ATGTATTGATACATGCACTT
1 ATGTATCGATACATGCACTT
*
474794 ATGTATCGATACAT-TACTTT
1 ATGTATCGATACATGCAC-TT
474814 ATTGTATCGATA
1 A-TGTATCGATA
474826 TAAATTGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 16 0.57
21 10 0.36
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATGCACTT
Found at i:476291 original size:52 final size:52
Alignment explanation
Indices: 475468--476302 Score: 714
Period size: 52 Copynumber: 16.1 Consensus size: 52
475458 GATACTAGAT
*
475468 TTAAAGATGATAAAGGTGCCAATGTGCTGATTCAAGGCCGAG-GACATTGGAC
1 TTAAAGATGATAAAGGTGCCAATATGCTGATTCAAGGCC-AGCGACATTGGAC
* *
475520 TTAAAGATGATAAAGGTGCCAATGTGCTGATTCAAGGCCAGGGACATTGGAC
1 TTAAAGATGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* * * * * *
475572 GTAAAGATGATAAAGGTGCTAATGTGCTGATTCAAAGCTAGCGATATTGGAC
1 TTAAAGATGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* *
475624 TTAAAGATGGTAAAGGTGCTAATATGCTGATTCAAGGCCAGCGACATTGGAC
1 TTAAAGATGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* * * * *
475676 TTAAAGATAATAAAGGTGCCAATATGCTAATTCAAGGCCAGCGAGATCGAAC
1 TTAAAGATGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* * * * *
475728 TTAAAGATAATAAATGTGCCAATATGCTAATTCAAGGCCTA-TGATATTGGAC
1 TTAAAGATGATAAAGGTGCCAATATGCTGATTCAAGGCC-AGCGACATTGGAC
* * * * * * * *
475780 TTAAAGATGAGAAAGATGCCAATATGTTCATTCAAAGCC-GATGATATTAGAC
1 TTAAAGATGATAAAGGTGCCAATATGCTGATTCAAGGCCAG-CGACATTGGAC
* * * * *
475832 TTAAAGATGAGAAAGATGCCAATACGCTGATTCAAGG-TAGTGACATTGGAC
1 TTAAAGATGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* * * * * * *
475883 TTAAAGGTGGT-AGGAGTGCTAATATGCTAATTCAAGGCCAGTGACATTAGAC
1 TTAAAGATGATAAAG-GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* * * * * * * * *
475935 TTAAAGATGAGAAAAGTGCTAATGTGCTGATTCAAAGCTAGTGACATTAGAT
1 TTAAAGATGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* * ** * * *
475987 TTAACGATAATAAAGGTGCCAATATGCAAATTCAAGGCCAACGATATTAGAC
1 TTAAAGATGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* * * * * * * **
476039 TTTAAGATGAGAATA-GTGCGATTCTACTGATTCAAGGCCAGTGACATTAAAC
1 TTAAAGATGATAA-AGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
** *
476091 TTAAAGATGATAAAGGTGTCCAATATGCTGATTCAAGGCCAAAGATATTGGAC
1 TTAAAGATGATAAAGGTG-CCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* * ** * * * * ** * **
476144 TTTAAGATGACAGGGGGTGCTAATGTACTAATTCAAGGCTTGTGACATTAAAC
1 TTAAAGATGATA-AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* * * * *
476197 TTAAAGAT-A-AGAAGATACCAATATGCTGATTCAAGGCTAGCAACATTGGAT
1 TTAAAGATGATA-AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* * * * *
476248 TTAAAGATGATAAAGATGTCAATATCCTGATTCAAGGCCAGCAATATTGGAC
1 TTAAAGATGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
476300 TTA
1 TTA
476303 GAAGGAGTTG
Statistics
Matches: 635, Mismatches: 134, Indels: 28
0.80 0.17 0.04
Matches are distributed among these distances:
50 2 0.00
51 74 0.12
52 486 0.77
53 69 0.11
54 4 0.01
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (52 bp):
TTAAAGATGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
Found at i:476485 original size:64 final size:63
Alignment explanation
Indices: 476354--476500 Score: 158
Period size: 64 Copynumber: 2.3 Consensus size: 63
476344 CACTAATTTA
*
476354 TGTGGGCTTTTGAAAAAGGGTTGCCACCGACTTATATGGGCTTTGGAAAAGGATGCCACCAACT
1 TGTGGACTTTTG-AAAAGGGTTGCCACCGACTTATATGGGCTTTGGAAAAGGATGCCACCAACT
* * * * *
476418 TGTGTAGACTTTTGAAAAGGGTTGCCA-CTACTTTTGTGGGCTTT-GAAAAGGGGTGCCA-TAGA
1 TGTG--GACTTTTGAAAAGGGTTGCCACCGACTTATATGGGCTTTGGAAAA-GGATGCCACCA-A
*
476480 GT
62 CT
476482 TGTGGAC-TTTGAAAAGGGT
1 TGTGGACTTTTGAAAAGGGT
476501 ACCATAGAGT
Statistics
Matches: 72, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
61 12 0.17
62 3 0.04
63 6 0.08
64 31 0.43
65 13 0.18
66 7 0.10
ACGTcount: A:0.25, C:0.14, G:0.31, T:0.30
Consensus pattern (63 bp):
TGTGGACTTTTGAAAAGGGTTGCCACCGACTTATATGGGCTTTGGAAAAGGATGCCACCAACT
Found at i:476510 original size:29 final size:29
Alignment explanation
Indices: 476428--476665 Score: 175
Period size: 29 Copynumber: 8.1 Consensus size: 29
476418 TGTGTAGACT
*** *
476428 TTTGAAAAGGGTTGCCACTACTTTTGTGGGC
1 TTTGAAAAGGG-TGCCA-TAGAGTTGTGGAC
476459 TTTGAAAAGGGGTGCCATAGAGTTGTGGAC
1 TTTGAAAA-GGGTGCCATAGAGTTGTGGAC
* *
476489 TTTGAAAAGGGTACCATAGAGTTGGGGAC
1 TTTGAAAAGGGTGCCATAGAGTTGTGGAC
* * * * *
476518 -TT-AAAAAGGTACCACAAAGTTATGGAC
1 TTTGAAAAGGGTGCCATAGAGTTGTGGAC
* *
476545 TTTGAAAAGAGTGCCA-CGAAGTTGTGGAC
1 TTTGAAAAGGGTGCCATAG-AGTTGTGGAC
*
476574 TTTAGAAAAGGGGTGCCAT-GAAG-T-T-GAA
1 TTT-GAAAA-GGGTGCCATAG-AGTTGTGGAC
* ** *
476602 TTTGGAGAAGGGTGCCACGGAGTTGTAGAC
1 TTT-GAAAAGGGTGCCATAGAGTTGTGGAC
476632 TTTAGAAAAGGGATGCCATAGAGTTGTGGAC
1 TTT-GAAAAGGG-TGCCATAGAGTTGTGGAC
476663 TTT
1 TTT
476666 AAGAAAAGTG
Statistics
Matches: 167, Mismatches: 28, Indels: 24
0.76 0.13 0.11
Matches are distributed among these distances:
27 30 0.18
28 15 0.09
29 42 0.25
30 35 0.21
31 42 0.25
32 3 0.02
ACGTcount: A:0.30, C:0.12, G:0.32, T:0.27
Consensus pattern (29 bp):
TTTGAAAAGGGTGCCATAGAGTTGTGGAC
Found at i:477117 original size:33 final size:33
Alignment explanation
Indices: 477080--477171 Score: 87
Period size: 32 Copynumber: 2.8 Consensus size: 33
477070 CCAACTTGTG
* *
477080 TAGGCTTTTGAAAATGGTTGCTACTGATTTATA
1 TAGGCTTTTGAAAAAGGTTGCTACTGACTTATA
* * * ** *
477113 TAGGC-TTTGAAAAAGGATACCACCAACTTATG
1 TAGGCTTTTGAAAAAGGTTGCTACTGACTTATA
* *
477145 TGGGCTTTTGAAAAGGGTTGCTACTGA
1 TAGGCTTTTGAAAAAGGTTGCTACTGA
477172 AAGCTCAAGG
Statistics
Matches: 43, Mismatches: 15, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
32 23 0.53
33 20 0.47
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34
Consensus pattern (33 bp):
TAGGCTTTTGAAAAAGGTTGCTACTGACTTATA
Found at i:479823 original size:19 final size:19
Alignment explanation
Indices: 479797--479835 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
479787 ATTCAATGAG
*
479797 ATGCTG-AACATATTAAAA
1 ATGCTGAAACATAATAAAA
479815 ATGCATGAAACATAATAAAA
1 ATGC-TGAAACATAATAAAA
479835 A
1 A
479836 AATGCATAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 2 0.11
20 12 0.67
ACGTcount: A:0.56, C:0.10, G:0.10, T:0.23
Consensus pattern (19 bp):
ATGCTGAAACATAATAAAA
Found at i:480726 original size:20 final size:20
Alignment explanation
Indices: 480701--480826 Score: 99
Period size: 20 Copynumber: 5.8 Consensus size: 20
480691 TTTTAACTAG
480701 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
480721 ATGTATCGATACATTTGGGTAAAAAGACAGA
1 ATGTATCGATACA-TT--G-----A-A-A-A
* *
480752 ATGTATCAATACATTGAAGA
1 ATGTATCGATACATTGAAAA
* * *
480772 ATGTATCGATACATTCATAC
1 ATGTATCGATACATTGAAAA
*
480792 ATGTATCGATACATAGAAAA
1 ATGTATCGATACATTGAAAA
480812 ATGTATCGATACATT
1 ATGTATCGATACATT
480827 TGGGTACTTT
Statistics
Matches: 83, Mismatches: 12, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
20 59 0.71
21 2 0.02
22 1 0.01
23 2 0.02
28 2 0.02
29 1 0.01
30 3 0.04
31 13 0.16
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:481601 original size:28 final size:28
Alignment explanation
Indices: 481517--482357 Score: 733
Period size: 28 Copynumber: 29.1 Consensus size: 28
481507 TGACATAGAG
* *
481517 AAAGTTGCCACCGACTTGTGTGGGCTTT-A
1 AAAGATGCCACTGAC-T-TGTGGGCTTTGA
* **
481546 AAAGGATGCCACTGACTTATGGATTTTGA
1 AAA-GATGCCACTGACTTGTGGGCTTTGA
* **
481575 AAAAATGCCTTTGACTTGTGGGCTTTGA
1 AAAGATGCCACTGACTTGTGGGCTTTGA
* * *
481603 AGAGATGCCACTGACTTGTGCGTTTTGA
1 AAAGATGCCACTGACTTGTGGGCTTTGA
* *
481631 AAGGATGCCACTGACTCGTGGGCTTTG-
1 AAAGATGCCACTGACTTGTGGGCTTTGA
* *
481658 GAAGAATGCCACTGACTTGTGGGCATTGA
1 AAAG-ATGCCACTGACTTGTGGGCTTTGA
*
481687 AGAGATGCCACTGACTTGTGCGG-TTTGA
1 AAAGATGCCACTGACTTGTG-GGCTTTGA
* *
481715 AAGGATGCCACTGACTCGTGGGCTTTGA
1 AAAGATGCCACTGACTTGTGGGCTTTGA
* * *
481743 AAAGGTGCCACTGACTTATGGGCTTGGA
1 AAAGATGCCACTGACTTGTGGGCTTTGA
*
481771 AAAGATGCCATTGACTTGTGGGCTTTGA
1 AAAGATGCCACTGACTTGTGGGCTTTGA
* * *
481799 AAAAATGCCACCGACTTGTGGGTTTTGA
1 AAAGATGCCACTGACTTGTGGGCTTTGA
*
481827 AAAGGATGCCACTGACTTGTGGACTTTGA
1 AAA-GATGCCACTGACTTGTGGGCTTTGA
*
481856 AAGGATGCCACTGA-TTGTGGGCTTT-A
1 AAAGATGCCACTGACTTGTGGGCTTTGA
* * *
481882 AAATGGTGCCACTGTCTTTTGGGCTTTGA
1 AAA-GATGCCACTGACTTGTGGGCTTTGA
** * * *
481911 AGGGGTGCCACTGATTTGTGGGCTTAGA
1 AAAGATGCCACTGACTTGTGGGCTTTGA
*
481939 AAAGGATGCCACTGACTTGTGGACTTTGA
1 AAA-GATGCCACTGACTTGTGGGCTTTGA
* *
481968 AAGGATGCTACTGACTTGTGGGCTTTGA
1 AAAGATGCCACTGACTTGTGGGCTTTGA
* * *
481996 AAGGGATGTCACTGACTTGTGGACTTTGA
1 AA-AGATGCCACTGACTTGTGGGCTTTGA
* * *
482025 AAGGATGCCACTGACTTATGGGCTTGGA
1 AAAGATGCCACTGACTTGTGGGCTTTGA
482053 AAAGATGCCACTGACTTGTGGGCTTTGA
1 AAAGATGCCACTGACTTGTGGGCTTTGA
* * * ** *
482081 AATGGGTTGCGACCAACTTGTGTGGGCTTTCA
1 AA--AGATGCCACTGAC-T-TGTGGGCTTTGA
* *
482113 AATGAGTTGCCACCGACTTGTGTGGGCTTTGA
1 AA--AGATGCCACTGAC-T-TGTGGGCTTTGA
*
482145 AATGATGCCACTGACTTGTGGGCTTTGA
1 AAAGATGCCACTGACTTGTGGGCTTTGA
* * *
482173 AATGGGTTGCCACCGACTTGTGTGGGCTTTGA
1 AA--AGATGCCACTGAC-T-TGTGGGCTTTGA
* ** *
482205 AACGAGTTGCCACCAACTTGTGTGGGCTTTCA
1 AA--AGATGCCACTGAC-T-TGTGGGCTTTGA
* *
482237 AATGAGTTGCCACCGACTTGTGTGGGCTTTGA
1 AA--AGATGCCACTGAC-T-TGTGGGCTTTGA
* * *
482269 AATGAGTTGCCACCGATTTGTGGGCTTTGA
1 AA--AGATGCCACTGACTTGTGGGCTTTGA
482299 AATA-ATGCCACTGACTTGTGGGCTTTGA
1 AA-AGATGCCACTGACTTGTGGGCTTTGA
* * *
482327 AAGGATGCCACTAATTTGTGGGCTTT-A
1 AAAGATGCCACTGACTTGTGGGCTTTGA
482354 AAAG
1 AAAG
482358 GGTGCCGCCA
Statistics
Matches: 679, Mismatches: 112, Indels: 44
0.81 0.13 0.05
Matches are distributed among these distances:
26 3 0.00
27 27 0.04
28 381 0.56
29 87 0.13
30 52 0.08
31 3 0.00
32 126 0.19
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (28 bp):
AAAGATGCCACTGACTTGTGGGCTTTGA
Found at i:481617 original size:56 final size:57
Alignment explanation
Indices: 481535--482600 Score: 761
Period size: 56 Copynumber: 18.6 Consensus size: 57
481525 CACCGACTTG
* * ** **
481535 TGTGGGCTTT-AAAAGGATGCCACTGACTTATGGATTTTGAAAAAATGCCTTTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACTTGTGGACTTTGAAAGGATGCCACTGACT
* *
481591 TGTGGGCTTTGAAGA-GATGCCACTGACTTGTGCG-TTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACTTGTG-GACTTTGAAAGGATGCCACTGACT
* * * * *
481647 CGTGGGCTTTG-GAAGAATGCCACTGACTTGTGGGCATTG-AAGAGATGCCACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACTTGTGGACTTTGAAAG-GATGCCACTGACT
* *
481703 TGTGCGG-TTTG-AAAGGATGCCACTGACTCGTGGGCTTTGAAAAGG-TGCCACTGACT
1 TGTG-GGCTTTGAAAAGGATGCCACTGACTTGTGGACTTTG-AAAGGATGCCACTGACT
* * * * ** *
481759 TATGGGCTTGGAAAA-GATGCCATTGACTTGTGGGCTTTGAAAAAATGCCACCGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACTTGTGGACTTTGAAAGGATGCCACTGACT
*
481815 TGTGGGTTTTGAAAAGGATGCCACTGACTTGTGGACTTTGAAAGGATGCCACTGA-T
1 TGTGGGCTTTGAAAAGGATGCCACTGACTTGTGGACTTTGAAAGGATGCCACTGACT
* * * * * *
481871 TGTGGGCTTT-AAAATGG-TGCCACTGTCTTTTGGGCTTTGAAGGGGTGCCACTGATT
1 TGTGGGCTTTGAAAA-GGATGCCACTGACTTGTGGACTTTGAAAGGATGCCACTGACT
* *
481927 TGTGGGCTTAGAAAAGGATGCCACTGACTTGTGGACTTTGAAAGGATGCTACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACTTGTGGACTTTGAAAGGATGCCACTGACT
* *
481984 TGTGGGCTTTGAAAGGGATGTCACTGACTTGTGGACTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACTTGTGGACTTTGAAAGGATGCCACTGACT
* * * * * **
482041 TATGGGCTTGGAAAA-GATGCCACTGACTTGTGGGCTTTGAAATGGGTTGCGACCAACTT
1 TGTGGGCTTTGAAAAGGATGCCACTGACTTGTGGACTTTGAAA--GGATGCCACTGAC-T
* * * * * *
482100 GTGTGGGCTTTCAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGATGCCACTGACT
1 -TGTGGGCTTTGAAAAG-GATGCCACTGAC-T-TGTGGACTTTGAAAGGATGCCACTGACT
* * * * * **
482161 TGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAACGAGTTGCCACCAACTT
1 TGTGGGCTTTGAAA-AGGATGCCACTGAC-T-TGTGGACTTTGAAA-G-GATGCCACTGAC-T
* * * * * * * *
482224 GTGTGGGCTTTCAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGAGTTGCCACCGATT
1 -TGTGGGCTTTGAAAAG-GATGCCACTGAC-T-TGTGGACTTTGAAA-G-GATGCCACTGACT
* * *
482287 TGTGGGCTTTGAAATA--ATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAATT
1 TGTGGGCTTTGAAA-AGGATGCCACTGACTTGTGGACTTTGAAAGGATGCCACTGACT
* * * * * * * *
482343 TGTGGGCTTT-AAAAGGGTGCCGCCACAGAGTTGTGGAC-TTAAAAGGATACTACAGGAGT
1 TGTGGGCTTTGAAAAGGAT---GCCACTGACTTGTGGACTTTGAAAGGATGCCAC-TGACT
** * * * * * *
482402 TACGGAC-TT-AAAAGGATGCCA-TAGAGTTGTGGAC-TTAAAAGGGTGCCACGGAAT
1 TGTGGGCTTTGAAAAGGATGCCACT-GACTTGTGGACTTTGAAAGGATGCCACTGACT
* * * * ** * *
482456 GGTGGACTTT-AAAA-GAGTGCCACGGAGTTGTGGACTTAAAAAGG-TGCCACGGAGT
1 TGTGGGCTTTGAAAAGGA-TGCCACTGACTTGTGGACTTTGAAAGGATGCCACTGACT
* * * * *
482511 TGTGGACTTT-AAAAGGGT-CCAC-GAAGTTGTGGACTTTAAAAGGATGCCA-TGGAGT
1 TGTGGGCTTTGAAAAGGATGCCACTG-ACTTGTGGACTTTGAAAGGATGCCACT-GACT
* * *
482566 TGTGGAC-TT-AAAAGGATGCCACGGAGTTGTGGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACTTGTGGACT
482601 CATGGAGTTG
Statistics
Matches: 844, Mismatches: 118, Indels: 97
0.80 0.11 0.09
Matches are distributed among these distances:
53 1 0.00
54 42 0.05
55 153 0.18
56 257 0.30
57 146 0.17
58 47 0.06
59 22 0.03
60 62 0.07
61 2 0.00
62 40 0.05
63 4 0.00
64 68 0.08
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (57 bp):
TGTGGGCTTTGAAAAGGATGCCACTGACTTGTGGACTTTGAAAGGATGCCACTGACT
Found at i:482107 original size:32 final size:32
Alignment explanation
Indices: 482069--482328 Score: 351
Period size: 32 Copynumber: 8.4 Consensus size: 32
482059 GCCACTGACT
* * *
482069 TGTGGGCTTTGAAATGGGTTGCGACCAACTTG
1 TGTGGGCTTTGAAATGAGTTGCCACCGACTTG
*
482101 TGTGGGCTTTCAAATGAGTTGCCACCGACTTG
1 TGTGGGCTTTGAAATGAGTTGCCACCGACTTG
*
482133 TGTGGGCTTTGAAATGA--TGCCACTGAC-T-
1 TGTGGGCTTTGAAATGAGTTGCCACCGACTTG
*
482161 TGTGGGCTTTGAAATGGGTTGCCACCGACTTG
1 TGTGGGCTTTGAAATGAGTTGCCACCGACTTG
* *
482193 TGTGGGCTTTGAAACGAGTTGCCACCAACTTG
1 TGTGGGCTTTGAAATGAGTTGCCACCGACTTG
*
482225 TGTGGGCTTTCAAATGAGTTGCCACCGACTTG
1 TGTGGGCTTTGAAATGAGTTGCCACCGACTTG
482257 TGTGGGCTTTGAAATGAGTTGCCACCGA-TT-
1 TGTGGGCTTTGAAATGAGTTGCCACCGACTTG
* *
482287 TGTGGGCTTTGAAAT-A-ATGCCACTGAC-T-
1 TGTGGGCTTTGAAATGAGTTGCCACCGACTTG
482315 TGTGGGCTTTGAAA
1 TGTGGGCTTTGAAA
482329 GGATGCCACT
Statistics
Matches: 206, Mismatches: 17, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
28 39 0.19
29 2 0.01
30 33 0.16
31 3 0.01
32 129 0.63
ACGTcount: A:0.20, C:0.18, G:0.30, T:0.32
Consensus pattern (32 bp):
TGTGGGCTTTGAAATGAGTTGCCACCGACTTG
Found at i:482358 original size:28 final size:28
Alignment explanation
Indices: 481535--482597 Score: 672
Period size: 28 Copynumber: 37.2 Consensus size: 28
481525 CACCGACTTG
481535 TGTGGGCTTTAAAAGGATGCCACTGACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* ** * **
481563 TATGGATTTTGAAAA-AATGCCTTTGACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
*
481591 TGTGGGCTTT-GAAGAGATGCCACTGACT
1 TGTGGGCTTTAAAAG-GATGCCACTGACT
* * *
481619 TGTGCGTTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* ** *
481647 CGTGGGCTTTGGAAGAATGCCACTGACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* *
481675 TGTGGGCATT-GAAGAGATGCCACTGACT
1 TGTGGGCTTTAAAAG-GATGCCACTGACT
*
481703 TGTGCGG-TTTGAAAGGATGCCACTGACT
1 TGTG-GGCTTTAAAAGGATGCCACTGACT
*
481731 CGTGGGCTTTGAAAAGG-TGCCACTGACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
* * *
481759 TATGGGCTTGGAAAA-GATGCCATTGACT
1 TGTGGGCTT-TAAAAGGATGCCACTGACT
* *
481787 TGTGGGCTTTGAAAA-AATGCCACCGACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
*
481815 TGTGGGTTTTGAAAAGGATGCCACTGACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
* *
481844 TGTGGACTTTGAAAGGATGCCACTGA-T
1 TGTGGGCTTTAAAAGGATGCCACTGACT
*
481871 TGTGGGCTTTAAAATGG-TGCCACTGTCT
1 TGTGGGCTTTAAAA-GGATGCCACTGACT
* * * * *
481899 TTTGGGCTTTGAAGGGGTGCCACTGATT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
*
481927 TGTGGGCTTAGAAAAGGATGCCACTGACT
1 TGTGGGCTT-TAAAAGGATGCCACTGACT
* * *
481956 TGTGGACTTTGAAAGGATGCTACTGACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* *
481984 TGTGGGCTTTGAAAGGGATGTCACTGACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
* *
482013 TGTGGACTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* *
482041 TATGGGCTTGGAAAA-GATGCCACTGACT
1 TGTGGGCTT-TAAAAGGATGCCACTGACT
* * * **
482069 TGTGGGCTTTGAAATGGGTTGCGACCAACTT
1 TGTGGGCTTT-AAA-AGGATGCCACTGAC-T
* * *
482100 GTGTGGGCTTTCAAATGAGTTGCCACCGACTT
1 -TGTGGGCTTT-AAAAG-GATGCCACTGAC-T
* *
482132 GTGTGGGCTTTGAAATGATGCCACTGACT
1 -TGTGGGCTTTAAAAGGATGCCACTGACT
* * *
482161 TGTGGGCTTTGAAATGGGTTGCCACCGACTT
1 TGTGGGCTTT-AAA-AGGATGCCACTGAC-T
* * **
482192 GTGTGGGCTTTGAAACGAGTTGCCACCAACTT
1 -TGTGGGCTTT-AAAAG-GATGCCACTGAC-T
* * *
482224 GTGTGGGCTTTCAAATGAGTTGCCACCGACTT
1 -TGTGGGCTTT-AAAAG-GATGCCACTGAC-T
* * * *
482256 GTGTGGGCTTTGAAATGAGTTGCCACCGATT
1 -TGTGGGCTTT-AAAAG-GATGCCACTGACT
* **
482287 TGTGGGCTTTGAAATAATGCCACTGACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* * *
482315 TGTGGGCTTTGAAAGGATGCCACTAATT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* * *
482343 TGTGGGCTTTAAAAGGGTGCCGCCACAGAGT
1 TGTGGGCTTTAAAAGGAT---GCCACTGACT
* * * * *
482374 TGTGGAC-TTAAAAGGATACTACAGGAGT
1 TGTGGGCTTTAAAAGGATGCCAC-TGACT
** * *
482402 TACGGAC-TTAAAAGGATGCCA-TAGAGT
1 TGTGGGCTTTAAAAGGATGCCACT-GACT
* * * *
482429 TGTGGAC-TTAAAAGGGTGCCACGGAAT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* * * *
482456 GGTGGACTTTAAAA-GAGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGA-TGCCACTGACT
* * * *
482484 TGTGGACTTAAAAAGG-TGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* * *
482511 TGTGGACTTTAAAAGGGT-CCAC-GAAGT
1 TGTGGGCTTTAAAAGGATGCCACTG-ACT
* *
482538 TGTGGACTTTAAAAGGATGCCA-TGGAGT
1 TGTGGGCTTTAAAAGGATGCCACT-GACT
* * *
482566 TGTGGAC-TTAAAAGGATGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
482593 TGTGG
1 TGTGG
482598 ACTCATGGAG
Statistics
Matches: 849, Mismatches: 141, Indels: 91
0.79 0.13 0.08
Matches are distributed among these distances:
26 3 0.00
27 138 0.16
28 430 0.51
29 91 0.11
30 47 0.06
31 20 0.02
32 120 0.14
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTAAAAGGATGCCACTGACT
Found at i:482436 original size:27 final size:27
Alignment explanation
Indices: 482364--482600 Score: 282
Period size: 27 Copynumber: 8.7 Consensus size: 27
482354 AAAGGGTGCC
*
482364 GCCACAGAGTTGTGGACTTAAAAGGAT
1 GCCACGGAGTTGTGGACTTAAAAGGAT
* * **
482391 ACTACAGGAGTTACGGACTTAAAAGGAT
1 GCCAC-GGAGTTGTGGACTTAAAAGGAT
** *
482419 GCCATAGAGTTGTGGACTTAAAAGGGT
1 GCCACGGAGTTGTGGACTTAAAAGGAT
* *
482446 GCCACGGAATGGTGGACTTTAAAA-GAGT
1 GCCACGGAGTTGTGGAC-TTAAAAGGA-T
482474 GCCACGGAGTTGTGGACTTAAAAAGG-T
1 GCCACGGAGTTGTGGACTT-AAAAGGAT
*
482501 GCCACGGAGTTGTGGACTTTAAAAGGGT
1 GCCACGGAGTTGTGGAC-TTAAAAGGAT
*
482529 -CCACGAAGTTGTGGACTTTAAAAGGAT
1 GCCACGGAGTTGTGGAC-TTAAAAGGAT
*
482556 GCCATGGAGTTGTGGACTTAAAAGGAT
1 GCCACGGAGTTGTGGACTTAAAAGGAT
482583 GCCACGGAGTTGTGGACT
1 GCCACGGAGTTGTGGACT
482601 CATGGAGTTG
Statistics
Matches: 178, Mismatches: 24, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
27 113 0.63
28 64 0.36
29 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.32, T:0.24
Consensus pattern (27 bp):
GCCACGGAGTTGTGGACTTAAAAGGAT
Found at i:482438 original size:55 final size:55
Alignment explanation
Indices: 482276--482754 Score: 377
Period size: 55 Copynumber: 8.9 Consensus size: 55
482266 TGAAATGAGT
* * * * ** * * * *
482276 TGCCACCGATTTGTGGGCTTTGAAATAATGCCACTGACTTGTGGGCTTTGAAAGGA
1 TGCCACGGAGTTGTGGACTTTAAAAGGATGCCACAGAGTTGTGGAC-TTAAAAGGA
** * * *
482332 TGCCACTAATTTGTGGGCTTTAAAAGGGTGCCGCCACAGAGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTTAAAAGGAT---GCCACAGAGTTGTGGACTTAAAAGGA
* * ** * *
482390 TACTACAGGAGTTACGGAC-TTAAAAGGATGCCATAGAGTTGTGGACTTAAAAGGG
1 TGCCAC-GGAGTTGTGGACTTTAAAAGGATGCCACAGAGTTGTGGACTTAAAAGGA
* * *
482445 TGCCACGGAATGGTGGACTTTAAAA-GAGTGCCACGGAGTTGTGGACTTAAAAAGG-
1 TGCCACGGAGTTGTGGACTTTAAAAGGA-TGCCACAGAGTTGTGGACTT-AAAAGGA
*
482500 TGCCACGGAGTTGTGGACTTTAAAAGGGT-CCAC-GAAGTTGTGGACTTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTTAAAAGGATGCCACAG-AGTTGTGGAC-TTAAAAGGA
* *
482555 TGCCATGGAGTTGTGGAC-TTAAAAGGATGCCACGGAGTTGTGGAC---------
1 TGCCACGGAGTTGTGGACTTTAAAAGGATGCCACAGAGTTGTGGACTTAAAAGGA
* ** * *
482600 T--CATGGAGTTGTGGAC-TTAAAAGGATGCCATGGAGTTATGGACTTTAGAAGGA
1 TGCCACGGAGTTGTGGACTTTAAAAGGATGCCACAGAGTTGTGGAC-TTAAAAGGA
** * *
482653 TGCCATTGAGTTGTAGAC-TTAAAAGGATGCCACAGAATTGTGGACTTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTTAAAAGGATGCCACAGAGTTGTGGAC-TTAAAAGGA
* *
482708 TGCTACGGAGTTGTGGAC-TTAAAAGGATGCCACGGAGTTGTGGACTT
1 TGCCACGGAGTTGTGGACTTTAAAAGGATGCCACAGAGTTGTGGACTT
482755 TGAAAAGAGA
Statistics
Matches: 349, Mismatches: 49, Indels: 52
0.78 0.11 0.12
Matches are distributed among these distances:
43 40 0.11
45 1 0.00
53 2 0.01
54 41 0.12
55 193 0.55
56 31 0.09
58 21 0.06
59 20 0.06
ACGTcount: A:0.29, C:0.14, G:0.31, T:0.26
Consensus pattern (55 bp):
TGCCACGGAGTTGTGGACTTTAAAAGGATGCCACAGAGTTGTGGACTTAAAAGGA
Found at i:482483 original size:82 final size:81
Alignment explanation
Indices: 482373--482754 Score: 416
Period size: 82 Copynumber: 4.8 Consensus size: 81
482363 CGCCACAGAG
* * ** **
482373 TTGTGGAC-TTAAAAGGATACTACAGGAGTTACGGACTTAAAAGGATGCCATAGAGTTGTGGACT
1 TTGTGGACTTTAAAAGGATGCCAC-GGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACT
482437 TAAAAGGGTGCCACGGAA
65 TAAAAGGGT-CCACGGAA
*
482455 TGGTGGACTTTAAAA-GAGTGCCACGGAGTTGTGGACTTAAAAAGG-TGCCACGGAGTTGTGGAC
1 TTGTGGACTTTAAAAGGA-TGCCACGGAGTTGTGGACTT-AAAAGGATGCCACGGAGTTGTGGAC
482518 TTTAAAAGGGTCCAC-GAA
64 -TTAAAAGGGTCCACGGAA
*
482536 GTTGTGGACTTTAAAAGGATGCCATGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGAC-
1 -TTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACT
* *
482600 --------T-CATGGAG
65 TAAAAGGGTCCACGGAA
* * * ** *
482608 TTGTGGAC-TTAAAAGGATGCCATGGAGTTATGGACTTTAGAAGGATGCCATTGAGTTGTAGACT
1 TTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGATGCCACGGAGTTGTGGACT
* *
482672 TAAAAGGATGCCACAGAA
65 TAAAAGGGT-CCACGGAA
*
482690 TTGTGGACTTTAAAAGGATGCTACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTT
1 TTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTT
482755 TGAAAAGAGA
Statistics
Matches: 253, Mismatches: 26, Indels: 42
0.79 0.08 0.13
Matches are distributed among these distances:
70 26 0.10
71 33 0.13
72 3 0.01
80 1 0.00
81 9 0.04
82 129 0.51
83 52 0.21
ACGTcount: A:0.30, C:0.13, G:0.31, T:0.26
Consensus pattern (81 bp):
TTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTT
AAAAGGGTCCACGGAA
Found at i:482619 original size:43 final size:43
Alignment explanation
Indices: 482558--482643 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
482548 AAAAGGATGC
*
482558 CATGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACT
1 CATGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTATGGACT
*
482601 CATGGAGTTGTGGACTTAAAAGGATGCCATGGAGTTATGGACT
1 CATGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTATGGACT
482644 TTAGAAGGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.27, C:0.13, G:0.34, T:0.27
Consensus pattern (43 bp):
CATGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTATGGACT
Found at i:482663 original size:28 final size:27
Alignment explanation
Indices: 482604--482754 Score: 203
Period size: 27 Copynumber: 5.5 Consensus size: 27
482594 GTGGACTCAT
*
482604 GGAGTTGTGGACTTAAAAGGATGCCAT
1 GGAGTTGTGGACTTAAAAGGATGCCAC
* * *
482631 GGAGTTATGGACTTTAGAAGGATGCCAT
1 GGAGTTGTGGAC-TTAAAAGGATGCCAC
* *
482659 TGAGTTGTAGACTTAAAAGGATGCCAC
1 GGAGTTGTGGACTTAAAAGGATGCCAC
* * *
482686 AGAATTGTGGACTTTAAAAGGATGCTAC
1 GGAGTTGTGGAC-TTAAAAGGATGCCAC
482714 GGAGTTGTGGACTTAAAAGGATGCCAC
1 GGAGTTGTGGACTTAAAAGGATGCCAC
482741 GGAGTTGTGGACTT
1 GGAGTTGTGGACTT
482755 TGAAAAGAGA
Statistics
Matches: 108, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
27 61 0.56
28 47 0.44
ACGTcount: A:0.30, C:0.12, G:0.31, T:0.27
Consensus pattern (27 bp):
GGAGTTGTGGACTTAAAAGGATGCCAC
Found at i:482664 original size:71 final size:71
Alignment explanation
Indices: 482535--482753 Score: 224
Period size: 71 Copynumber: 2.9 Consensus size: 71
482525 GGGTCCACGA
* *
482535 AGTTGTGGACTTTAAAAGGATGCCATGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGAC
1 AGTTGTGGACTTTAAAAGGATGCCATGGAGTTATGGACTTAAAAGGATGCCACGGAGTTGTAGAC
482600 TCATGG
66 TCATGG
* **
482606 AGTTGTGGAC-TTAAAAGGATGCCATGGAGTTATGGACTTTAGAAGGATGCCATTGAGTTGTAGA
1 AGTTGTGGACTTTAAAAGGATGCCATGGAGTTATGGAC-TTAAAAGGATGCCACGGAGTTGTAGA
*
482670 CTTAAAAGGATGCCACAG
65 C-T-----CATG-----G
* * * * *
482688 AATTGTGGACTTTAAAAGGATGCTACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGAC
1 AGTTGTGGACTTTAAAAGGATGCCATGGAGTTATGGACTTAAAAGGATGCCACGGAGTTGTAGAC
482753 T
66 T
482754 TTGAAAAGAG
Statistics
Matches: 121, Mismatches: 14, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
70 26 0.21
71 33 0.27
72 1 0.01
77 3 0.02
81 1 0.01
82 33 0.27
83 24 0.20
ACGTcount: A:0.29, C:0.12, G:0.32, T:0.27
Consensus pattern (71 bp):
AGTTGTGGACTTTAAAAGGATGCCATGGAGTTATGGACTTAAAAGGATGCCACGGAGTTGTAGAC
TCATGG
Found at i:482675 original size:98 final size:98
Alignment explanation
Indices: 482506--482698 Score: 289
Period size: 98 Copynumber: 2.0 Consensus size: 98
482496 AAGGTGCCAC
* * *
482506 GGAGTTGTGGACTTTAAAAGGGTCCACGAAGTTGTGGACTTTAAAAGGATGCCATGGAGTTGTGG
1 GGAGTTGTGGACTTTAAAAGGATCCACGAAGTTATGGACTTTAAAAGGATGCCATGGAGTTGTAG
* *
482571 ACTTAAAAGGATGCCACGGAGTTGTGGACTCAT
66 ACTTAAAAGGATGCCACAGAATTGTGGACTCAT
* * * *
482604 GGAGTTGTGGAC-TTAAAAGGATGCCATGGAGTTATGGACTTTAGAAGGATGCCATTGAGTTGTA
1 GGAGTTGTGGACTTTAAAAGGAT-CCACGAAGTTATGGACTTTAAAAGGATGCCATGGAGTTGTA
482668 GACTTAAAAGGATGCCACAGAATTGTGGACT
65 GACTTAAAAGGATGCCACAGAATTGTGGACT
482699 TTAAAAGGAT
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
97 9 0.11
98 76 0.89
ACGTcount: A:0.29, C:0.12, G:0.32, T:0.27
Consensus pattern (98 bp):
GGAGTTGTGGACTTTAAAAGGATCCACGAAGTTATGGACTTTAAAAGGATGCCATGGAGTTGTAG
ACTTAAAAGGATGCCACAGAATTGTGGACTCAT
Done.