Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold320
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: 2598547
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 499 characters in sequence are not A, C, G, or T
File 10 of 17
Found at i:1412181 original size:12 final size:13
Alignment explanation
Indices: 1412158--1412187 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1412148 GACTACTCCT
1412158 ATCATAATGACTA
1 ATCATAATGACTA
1412171 ATCAT-ATGACTA
1 ATCATAATGACTA
1412183 ATCAT
1 ATCAT
1412188 CACTAGAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (13 bp):
ATCATAATGACTA
Found at i:1412924 original size:22 final size:23
Alignment explanation
Indices: 1412897--1412940 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1412887 AAACATCGGC
1412897 TATTATCA-TATGTTCAAAGCGT
1 TATTATCATTATGTTCAAAGCGT
1412919 TATTATCATTATGTTCAAAGCG
1 TATTATCATTATGTTCAAAGCG
1412941 AGCGTTGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (23 bp):
TATTATCATTATGTTCAAAGCGT
Found at i:1419311 original size:3 final size:3
Alignment explanation
Indices: 1419303--1419333 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1419293 CAAGTCAACT
*
1419303 TCA TCA TCA TCA TCA TTA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1419334 TGATGGTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (3 bp):
TCA
Found at i:1419323 original size:15 final size:15
Alignment explanation
Indices: 1419305--1419334 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1419295 AGTCAACTTC
1419305 ATCATCATCATCATT
1 ATCATCATCATCATT
1419320 ATCATCATCATCATT
1 ATCATCATCATCATT
1419335 GATGGTTGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.40
Consensus pattern (15 bp):
ATCATCATCATCATT
Found at i:1432988 original size:79 final size:78
Alignment explanation
Indices: 1432856--1433183 Score: 288
Period size: 79 Copynumber: 4.1 Consensus size: 78
1432846 ACAACGGGGC
1432856 TGGAGTATCCCTTGATTATGGAAAATCGGTGTTCTAGAAACAAAATCTGGGTTGGAGTATCCCCT
1 TGGAGTATCCC-TGATTAT-GAAAATCGGTGTTCTAGAAACAAAATCTGGGTTGGAGTATCCCCT
*
1432921 TGAAAATAACAGGG-T
64 CGAAAATAAC-GGGAT
* * * *
1432936 TGGAGCATCCCTGATTATAGAAAATTGGTGTT-TTGAAAATAAAATC-GAGGTTGGAGTATCCCC
1 TGGAGTATCCCTGATTAT-GAAAATCGGTGTTCTAG-AAACAAAATCTG-GGTTGGAGTATCCCC
1432999 TCGAAAATAACGGGAT
63 TCGAAAATAACGGGAT
* ** * *** * *
1433015 TGGAGTATCCCCGATTATGAAAAATCGAAGCTT-TAGAAATAAGGCCAGGGTTGGAGTATCCCCG
1 TGGAGTATCCCTGATTATG-AAAATCGGTG-TTCTAGAAACAAAATCTGGGTTGGAGTATCCCCT
* *
1433079 CCAAAATAACGGGGT
64 CGAAAATAACGGGAT
* ** * ** * * * * *
1433094 TGAAGTATCCCCAATTGTGAGAAATCAATATTTTAGAAATAAAGTCGGGGTTGGAGTATCCCCTC
1 TGGAGTATCCCTGATTATGA-AAATCGGTGTTCTAGAAACAAAATCTGGGTTGGAGTATCCCCTC
1433159 -AGAAATAACGGGAT
65 GA-AAATAACGGGAT
1433173 TGGAGTATCCC
1 TGGAGTATCCC
1433184 GACTATAAAA
Statistics
Matches: 209, Mismatches: 30, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
78 11 0.05
79 183 0.88
80 15 0.07
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (78 bp):
TGGAGTATCCCTGATTATGAAAATCGGTGTTCTAGAAACAAAATCTGGGTTGGAGTATCCCCTCG
AAAATAACGGGAT
Found at i:1435686 original size:62 final size:63
Alignment explanation
Indices: 1435589--1435717 Score: 179
Period size: 62 Copynumber: 2.1 Consensus size: 63
1435579 AATATGCCTG
* * * * *
1435589 AATGTATCGATACATTAAAAAATGTATCGATACATCTGGAT-AAACCCAGAATGTATCGATAC
1 AATGTATCAATACAGTAAAAAATGTATCAATACATCTGGATAAAACCCAAAATATATCGATAC
* * *
1435651 AATGTATCAATACAGTGAACAATGTATCAATACATCTGGGTAAAACCCAAAATATATCGATAC
1 AATGTATCAATACAGTAAAAAATGTATCAATACATCTGGATAAAACCCAAAATATATCGATAC
1435714 AATG
1 AATG
1435718 AATAATGTAT
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
62 35 0.60
63 23 0.40
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.26
Consensus pattern (63 bp):
AATGTATCAATACAGTAAAAAATGTATCAATACATCTGGATAAAACCCAAAATATATCGATAC
Found at i:1436412 original size:41 final size:41
Alignment explanation
Indices: 1436322--1436481 Score: 150
Period size: 41 Copynumber: 3.9 Consensus size: 41
1436312 GGGGGCGTCC
** *
1436322 TGCTCTTTGAGGATTAAGG-AAAAGGAGAATGAAATAGATTC-
1 TGCTCTTTGAGGACAAAGGAAAAAGGAGAATAAAAT-GA-TCA
1436363 TGCTCTTTGAGGACAAAGGAAAAAGGA-AATAAAATGAATCA
1 TGCTCTTTGAGGACAAAGGAAAAAGGAGAATAAAATG-ATCA
* *
1436404 TGCCCTTTGAAGACAAAGGAAAAAGGA-AATTAAATATG-TCA
1 TGCTCTTTGAGGACAAAGGAAAAAGGAGAA-TAAA-ATGATCA
* * * * *
1436445 TACTTTTTTAGAACAAAGGAACAAGGAGAATAAAATG
1 TGCTCTTTGAGGACAAAGGAAAAAGGAGAATAAAATG
1436482 CGTCCTATTT
Statistics
Matches: 101, Mismatches: 12, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
40 6 0.06
41 79 0.78
42 13 0.13
43 3 0.03
ACGTcount: A:0.46, C:0.09, G:0.22, T:0.23
Consensus pattern (41 bp):
TGCTCTTTGAGGACAAAGGAAAAAGGAGAATAAAATGATCA
Found at i:1436493 original size:41 final size:42
Alignment explanation
Indices: 1436368--1436500 Score: 114
Period size: 41 Copynumber: 3.2 Consensus size: 42
1436358 GATTCTGCTC
* * * **
1436368 TTTGAGGACAAAGGAAAAAGGAAATAAAATGA-ATCATGC-CC
1 TTTGAGAACAAAGGAAAAAGGAAATAAAAT-ACGTCATACTTT
* *
1436409 TTTGA-AGACAAAGGAAAAAGGAAATTAAATATGTCATACTTT
1 TTTGAGA-ACAAAGGAAAAAGGAAATAAAATACGTCATACTTT
* * *
1436451 TTT-AGAACAAAGGAACAAGGAGAATAAAATGCGTCCTA-TTT
1 TTTGAGAACAAAGGAAAAAGGA-AATAAAATACGTCATACTTT
1436492 TTTGAGAAC
1 TTTGAGAAC
1436501 TAGAAGGGAA
Statistics
Matches: 75, Mismatches: 11, Indels: 11
0.77 0.11 0.11
Matches are distributed among these distances:
40 1 0.01
41 53 0.71
42 21 0.28
ACGTcount: A:0.46, C:0.11, G:0.20, T:0.24
Consensus pattern (42 bp):
TTTGAGAACAAAGGAAAAAGGAAATAAAATACGTCATACTTT
Found at i:1436733 original size:61 final size:61
Alignment explanation
Indices: 1436629--1436764 Score: 175
Period size: 61 Copynumber: 2.2 Consensus size: 61
1436619 GGACATAGGA
* *
1436629 GAAAAGGAAAAGGGGTCCTACTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGCGAGCTTT
1 GAAAA-GAAAAGGCGTCCTACTCTTTGAGGACTAAAAAGTGCCAACAACTCGTGCGAGCTTT
* * * *
1436691 GAAAAGAAAAGGCGTCCTACTCTTTGATGACT-AAAGGATGCCAACAACTCGTGTGGGCTTT
1 GAAAAGAAAAGGCGTCCTACTCTTTGAGGACTAAAAAG-TGCCAACAACTCGTGCGAGCTTT
*
1436752 GAAAGAGGAAAGG
1 GAAA-AGAAAAGG
1436765 AAATGAGTAG
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
60 4 0.06
61 49 0.75
62 12 0.18
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.21
Consensus pattern (61 bp):
GAAAAGAAAAGGCGTCCTACTCTTTGAGGACTAAAAAGTGCCAACAACTCGTGCGAGCTTT
Found at i:1437098 original size:41 final size:41
Alignment explanation
Indices: 1437008--1437167 Score: 150
Period size: 41 Copynumber: 3.9 Consensus size: 41
1436998 GGGGGCGTCC
** *
1437008 TGCTCTTTGAGGATTAAGG-AAAAGGAGAATGAAATAGATTC-
1 TGCTCTTTGAGGACAAAGGAAAAAGGAGAATAAAAT-GA-TCA
1437049 TGCTCTTTGAGGACAAAGGAAAAAGGA-AATAAAATGAATCA
1 TGCTCTTTGAGGACAAAGGAAAAAGGAGAATAAAATG-ATCA
* *
1437090 TGCCCTTTGAAGACAAAGGAAAAAGGA-AATTAAATATG-TCA
1 TGCTCTTTGAGGACAAAGGAAAAAGGAGAA-TAAA-ATGATCA
* * * * *
1437131 TACTTTTTTAGAACAAAGGAACAAGGAGAATAAAATG
1 TGCTCTTTGAGGACAAAGGAAAAAGGAGAATAAAATG
1437168 CGTCCTATTT
Statistics
Matches: 101, Mismatches: 12, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
40 6 0.06
41 79 0.78
42 13 0.13
43 3 0.03
ACGTcount: A:0.46, C:0.09, G:0.22, T:0.23
Consensus pattern (41 bp):
TGCTCTTTGAGGACAAAGGAAAAAGGAGAATAAAATGATCA
Found at i:1437179 original size:41 final size:42
Alignment explanation
Indices: 1437054--1437186 Score: 114
Period size: 41 Copynumber: 3.2 Consensus size: 42
1437044 GATTCTGCTC
* * * **
1437054 TTTGAGGACAAAGGAAAAAGGAAATAAAATGA-ATCATGC-CC
1 TTTGAGAACAAAGGAAAAAGGAAATAAAAT-ACGTCATACTTT
* *
1437095 TTTGA-AGACAAAGGAAAAAGGAAATTAAATATGTCATACTTT
1 TTTGAGA-ACAAAGGAAAAAGGAAATAAAATACGTCATACTTT
* * *
1437137 TTT-AGAACAAAGGAACAAGGAGAATAAAATGCGTCCTA-TTT
1 TTTGAGAACAAAGGAAAAAGGA-AATAAAATACGTCATACTTT
1437178 TTTGAGAAC
1 TTTGAGAAC
1437187 TAGAAGGGAA
Statistics
Matches: 75, Mismatches: 11, Indels: 11
0.77 0.11 0.11
Matches are distributed among these distances:
40 1 0.01
41 53 0.71
42 21 0.28
ACGTcount: A:0.46, C:0.11, G:0.20, T:0.24
Consensus pattern (42 bp):
TTTGAGAACAAAGGAAAAAGGAAATAAAATACGTCATACTTT
Found at i:1437419 original size:61 final size:62
Alignment explanation
Indices: 1437315--1437448 Score: 164
Period size: 61 Copynumber: 2.2 Consensus size: 62
1437305 GGACATAGGA
* * *
1437315 GAAAAGGAAAAGGGGTCCTACTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGCGAGCTTT
1 GAAAAGGAAAAGGCGTCCTACTCTTTGAGAACTAAAAAGTGCCAACAACTCGTGCGAGCTTT
* * * * *
1437377 GAAAA-GAAAAGGCGTCCTGCTCTTTGATAACT-AAAGGATGCCAACAACTCGTGTGGGCTTT
1 GAAAAGGAAAAGGCGTCCTACTCTTTGAGAACTAAAAAG-TGCCAACAACTCGTGCGAGCTTT
1437438 GAAAGAGGAAA
1 GAAA-AGGAAA
1437449 GAAAATGAGT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
60 4 0.07
61 47 0.77
62 6 0.10
63 4 0.07
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (62 bp):
GAAAAGGAAAAGGCGTCCTACTCTTTGAGAACTAAAAAGTGCCAACAACTCGTGCGAGCTTT
Found at i:1437521 original size:686 final size:686
Alignment explanation
Indices: 1436209--1437585 Score: 2691
Period size: 686 Copynumber: 2.0 Consensus size: 686
1436199 CTCCTTAGAT
1436209 AGGTGTTGGTTACTGTAAACTCTGGAAAGGTTGGCCACCAACTTATGTGGGCTTTTTGGGTGCCG
1 AGGTGTTGGTTACTGTAAACTCTGGAAAGGTTGGCCACCAACTTATGTGGGCTTTTTGGGTGCCG
1436274 CCAACTTGTGCGGACTTTGAAAGAGGAAAGAAAAGGAAGGGGGCGTCCTGCTCTTTGAGGATTAA
66 CCAACTTGTGCGGACTTTGAAAGAGGAAAGAAAAGGAAGGGGGCGTCCTGCTCTTTGAGGATTAA
1436339 GGAAAAGGAGAATGAAATAGATTCTGCTCTTTGAGGACAAAGGAAAAAGGAAATAAAATGAATCA
131 GGAAAAGGAGAATGAAATAGATTCTGCTCTTTGAGGACAAAGGAAAAAGGAAATAAAATGAATCA
1436404 TGCCCTTTGAAGACAAAGGAAAAAGGAAATTAAATATGTCATACTTTTTTAGAACAAAGGAACAA
196 TGCCCTTTGAAGACAAAGGAAAAAGGAAATTAAATATGTCATACTTTTTTAGAACAAAGGAACAA
* *
1436469 GGAGAATAAAATGCGTCCTATTTTTTGAGAACTAGAAGGGAAAATAAGGAAATGAAGTGCGTCTT
261 GGAGAATAAAATGCGTCCTATTTTTTGAGAACTAGAAGGGAAAATAAGGAAATGAAGTGCATCCT
1436534 GTTCTTTGAGGACAAGAAAAAAAAGCATCCTGCTCTTTGAGAACAAAAGGGAAAAGAAGGAAATG
326 GTTCTTTGAGGACAAGAAAAAAAAGCATCCTGCTCTTTGAGAACAAAAGGGAAAAGAAGGAAATG
*
1436599 AATTGTGTCCTGCTCTTTGAGGACATAGGAGAAAAGGAAAAGGGGTCCTACTCTTTGAGGACTAA
391 AAATGTGTCCTGCTCTTTGAGGACATAGGAGAAAAGGAAAAGGGGTCCTACTCTTTGAGGACTAA
*
1436664 AAAGTGCCACCAACTCGTGCGAGCTTTGAAAAGAAAAGGCGTCCTACTCTTTGATGACTAAAGGA
456 AAAGTGCCACCAACTCGTGCGAGCTTTGAAAAGAAAAGGCGTCCTACTCTTTGATAACTAAAGGA
*
1436729 TGCCAACAACTCGTGTGGGCTTTGAAAGAGGAAAGGAAATGAGTAGGTATCCTGCTCTTTGAAGA
521 TGCCAACAACTCGTGTGGGCTTTGAAAGAGGAAAGAAAATGAGTAGGTATCCTGCTCTTTGAAGA
1436794 CAAAGGAAAAAGGAAAATGAAATGCATCTTGCTCTTTGAGGACAAAGAAGAAAAGGAAAAGGCGT
586 CAAAGGAAAAAGGAAAATGAAATGCATCTTGCTCTTTGAGGACAAAGAAGAAAAGGAAAAGGCGT
1436859 CTTACTCTTTGAAGACTAAGGGAGAAGAAGGAAATA
651 CTTACTCTTTGAAGACTAAGGGAGAAGAAGGAAATA
*
1436895 AGGTGTTGGTTACTGTAAACTCTGGAAAGGTTGGCCACCAACTTATGTGGGCTTTTTGGGTGTCG
1 AGGTGTTGGTTACTGTAAACTCTGGAAAGGTTGGCCACCAACTTATGTGGGCTTTTTGGGTGCCG
1436960 CCAACTTGTGCGGACTTTGAAAGAGGAAAGAAAAGGAAGGGGGCGTCCTGCTCTTTGAGGATTAA
66 CCAACTTGTGCGGACTTTGAAAGAGGAAAGAAAAGGAAGGGGGCGTCCTGCTCTTTGAGGATTAA
1437025 GGAAAAGGAGAATGAAATAGATTCTGCTCTTTGAGGACAAAGGAAAAAGGAAATAAAATGAATCA
131 GGAAAAGGAGAATGAAATAGATTCTGCTCTTTGAGGACAAAGGAAAAAGGAAATAAAATGAATCA
1437090 TGCCCTTTGAAGACAAAGGAAAAAGGAAATTAAATATGTCATACTTTTTTAGAACAAAGGAACAA
196 TGCCCTTTGAAGACAAAGGAAAAAGGAAATTAAATATGTCATACTTTTTTAGAACAAAGGAACAA
1437155 GGAGAATAAAATGCGTCCTATTTTTTGAGAACTAGAAGGGAAAATAAGGAAATGAAGTGCATCCT
261 GGAGAATAAAATGCGTCCTATTTTTTGAGAACTAGAAGGGAAAATAAGGAAATGAAGTGCATCCT
1437220 GTTCTTTGAGGACAAGAAAAAAAAGCATCCTGCTCTTTGAGAACAAAAGGGAAAAGAAGGAAATG
326 GTTCTTTGAGGACAAGAAAAAAAAGCATCCTGCTCTTTGAGAACAAAAGGGAAAAGAAGGAAATG
1437285 AAATGTGTCCTGCTCTTTGAGGACATAGGAGAAAAGGAAAAGGGGTCCTACTCTTTGAGGACTAA
391 AAATGTGTCCTGCTCTTTGAGGACATAGGAGAAAAGGAAAAGGGGTCCTACTCTTTGAGGACTAA
*
1437350 AAAGTGCCACCAACTCGTGCGAGCTTTGAAAAGAAAAGGCGTCCTGCTCTTTGATAACTAAAGGA
456 AAAGTGCCACCAACTCGTGCGAGCTTTGAAAAGAAAAGGCGTCCTACTCTTTGATAACTAAAGGA
1437415 TGCCAACAACTCGTGTGGGCTTTGAAAGAGGAAAGAAAATGAGTAGGTATCCTGCTCTTTGAAGA
521 TGCCAACAACTCGTGTGGGCTTTGAAAGAGGAAAGAAAATGAGTAGGTATCCTGCTCTTTGAAGA
1437480 CAAAGGAAAAAGGAAAATGAAATGCATCTTGCTCTTTGAGGACAAAGAAGAAAAGGAAAAGGCGT
586 CAAAGGAAAAAGGAAAATGAAATGCATCTTGCTCTTTGAGGACAAAGAAGAAAAGGAAAAGGCGT
1437545 CTTACTCTTTGAAGACTAAGGGAGAAGAAGGAAATA
651 CTTACTCTTTGAAGACTAAGGGAGAAGAAGGAAATA
1437581 AGGTG
1 AGGTG
1437586 CACCCTGCTA
Statistics
Matches: 684, Mismatches: 7, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
686 684 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (686 bp):
AGGTGTTGGTTACTGTAAACTCTGGAAAGGTTGGCCACCAACTTATGTGGGCTTTTTGGGTGCCG
CCAACTTGTGCGGACTTTGAAAGAGGAAAGAAAAGGAAGGGGGCGTCCTGCTCTTTGAGGATTAA
GGAAAAGGAGAATGAAATAGATTCTGCTCTTTGAGGACAAAGGAAAAAGGAAATAAAATGAATCA
TGCCCTTTGAAGACAAAGGAAAAAGGAAATTAAATATGTCATACTTTTTTAGAACAAAGGAACAA
GGAGAATAAAATGCGTCCTATTTTTTGAGAACTAGAAGGGAAAATAAGGAAATGAAGTGCATCCT
GTTCTTTGAGGACAAGAAAAAAAAGCATCCTGCTCTTTGAGAACAAAAGGGAAAAGAAGGAAATG
AAATGTGTCCTGCTCTTTGAGGACATAGGAGAAAAGGAAAAGGGGTCCTACTCTTTGAGGACTAA
AAAGTGCCACCAACTCGTGCGAGCTTTGAAAAGAAAAGGCGTCCTACTCTTTGATAACTAAAGGA
TGCCAACAACTCGTGTGGGCTTTGAAAGAGGAAAGAAAATGAGTAGGTATCCTGCTCTTTGAAGA
CAAAGGAAAAAGGAAAATGAAATGCATCTTGCTCTTTGAGGACAAAGAAGAAAAGGAAAAGGCGT
CTTACTCTTTGAAGACTAAGGGAGAAGAAGGAAATA
Found at i:1437677 original size:45 final size:45
Alignment explanation
Indices: 1437569--1437921 Score: 300
Period size: 45 Copynumber: 8.1 Consensus size: 45
1437559 ACTAAGGGAG
** *
1437569 AAGAAGGAAAT-AAGGTGCACCCTGCTATTTGAGGAC-AAAG-G-A
1 AAGAAGGAAATGAA-GTGCGTCCTGCTCTTTGAGGACAAAAGAGAA
* *
1437611 AA-AAGGAAATAAAGTACGTCCTGCTCTTTGAGGACAAAAGAGAA
1 AAGAAGGAAATGAAGTGCGTCCTGCTCTTTGAGGACAAAAGAGAA
* * * *
1437655 AAGAAGGAAATGAAGTGTGTCCTGCTCTTTGAGGAC-AATGTGAC
1 AAGAAGGAAATGAAGTGCGTCCTGCTCTTTGAGGACAAAAGAGAA
* * * * *
1437699 AATAAGAAAATGAGGTACGCCCTGCTCTTTGAGGAC-AAAG-GAA
1 AAGAAGGAAATGAAGTGCGTCCTGCTCTTTGAGGACAAAAGAGAA
* * * * * *
1437742 AA-AA-AAAATGAAATGTGCCCTACTCTTTGTA-GACAAATGA-AA
1 AAGAAGGAAATGAAGTGCGTCCTGCTCTTTG-AGGACAAAAGAGAA
** ** *
1437784 AATGAAAAAAAAAAAGTGCGTCCTGTTCTTTGAGGACAAAAGAGAA
1 AA-GAAGGAAATGAAGTGCGTCCTGCTCTTTGAGGACAAAAGAGAA
* * *
1437830 AAGAAGGAAATGAAGTGCATCCTACTCTTTGAGGACAAAAG-GAC
1 AAGAAGGAAATGAAGTGCGTCCTGCTCTTTGAGGACAAAAGAGAA
* * * *
1437874 AAGAAAGAAATGAAATGTGTCCTGCTCTTTGAGGACAAAGGAGAA
1 AAGAAGGAAATGAAGTGCGTCCTGCTCTTTGAGGACAAAAGAGAA
1437919 AAG
1 AAG
1437922 GAAAAAATGT
Statistics
Matches: 250, Mismatches: 47, Indels: 25
0.78 0.15 0.08
Matches are distributed among these distances:
41 49 0.20
42 18 0.07
43 5 0.02
44 81 0.32
45 93 0.37
46 4 0.02
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (45 bp):
AAGAAGGAAATGAAGTGCGTCCTGCTCTTTGAGGACAAAAGAGAA
Found at i:1437725 original size:44 final size:41
Alignment explanation
Indices: 1437465--1437925 Score: 232
Period size: 44 Copynumber: 10.8 Consensus size: 41
1437455 GAGTAGGTAT
* * * **
1437465 CCTGCTCTTTGAAGACAAAGGAAAAAGGAAAATGAAATGCAT
1 CCTGCTCTTTGAGGACAAAGGAAAAAGG-AAATGAAGTACGC
* * * *
1437507 CTTGCTCTTTGAGGACAAAGAAGAAAAGG-AA--AAG-GCGT
1 CCTGCTCTTTGAGGACAAAGGA-AAAAGGAAATGAAGTACGC
* * * * * *
1437545 CTTACTCTTTGAAGACTAAGGGAGAAGAAGGAAAT-AAGGTGCAC
1 CCTGCTCTTTGAGGAC-AAAGGA-AA-AAGGAAATGAA-GTACGC
* * *
1437589 CCTGCTATTTGAGGACAAAGGAAAAAGGAAATAAAGTACGT
1 CCTGCTCTTTGAGGACAAAGGAAAAAGGAAATGAAGTACGC
** *
1437630 CCTGCTCTTTGAGGACAAAAGAGAAAAGAAGGAAATGAAGTGTGT
1 CCTGCTCTTTGAGGAC-AAAG-G-AAA-AAGGAAATGAAGTACGC
* * *
1437675 CCTGCTCTTTGAGGACAATGTGACAATAAGAAAATGAGGTACGC
1 CCTGCTCTTTGAGGACAAAG-GA-AA-AAGGAAATGAAGTACGC
** * **
1437719 CCTGCTCTTTGAGGACAAAGGAAAAAAAAAATGAAATGTGC
1 CCTGCTCTTTGAGGACAAAGGAAAAAGGAAATGAAGTACGC
* * * ** * *
1437760 CCTACTCTTTGTA-GACAAATGAAAAATGAAAAAAAAAAAGTGCGT
1 CCTGCTCTTTG-AGGACAAAGGAAAAA-G---GAAATGAAGTACGC
* * **
1437805 CCTGTTCTTTGAGGACAAAAGAGAAAAGAAGGAAATGAAGTGCAT
1 CCTGCTCTTTGAGGAC-AAAG-G-AAA-AAGGAAATGAAGTACGC
* * * ** *
1437850 CCTACTCTTTGAGGACAAAAGGACAAGAAAGAAATGAAATGTGT
1 CCTGCTCTTTGAGGAC-AAAGGA-AA-AAGGAAATGAAGTACGC
1437894 CCTGCTCTTTGAGGACAAAGGAGAAAAGGAAA
1 CCTGCTCTTTGAGGACAAAGGA-AAAAGGAAA
1437926 AAATGTCCTA
Statistics
Matches: 334, Mismatches: 61, Indels: 48
0.75 0.14 0.11
Matches are distributed among these distances:
38 17 0.05
39 9 0.03
40 4 0.01
41 64 0.19
42 38 0.11
43 25 0.07
44 87 0.26
45 80 0.24
46 3 0.01
47 1 0.00
48 4 0.01
49 2 0.01
ACGTcount: A:0.42, C:0.14, G:0.25, T:0.20
Consensus pattern (41 bp):
CCTGCTCTTTGAGGACAAAGGAAAAAGGAAATGAAGTACGC
Found at i:1437734 original size:130 final size:127
Alignment explanation
Indices: 1437465--1437921 Score: 424
Period size: 130 Copynumber: 3.5 Consensus size: 127
1437455 GAGTAGGTAT
* * ** *
1437465 CCTGCTCTTTGAAGACAAAGGAAAAAGGAAAATGAAATGCATCTTGCTCTTTGAGGAC-AAAGAA
1 CCTGCTCTTTGAGGACAAAGGAAAAAAG-AAATGAAATGTGTCCTGCTCTTTGAGGACAAAAGAA
* * * * * * * *
1437529 GAA-AAGG-AAAAG-GCGTCTTACTCTTTGAAGACTAAGGGAGAAGAAGGAAATAAGGTGCAC
65 AAAGAAGGAAAAAGTGCGTCCTGCTCTTTGAGGACAAAGAGAAAAGAAGGAAATGAGGTGCAC
* *
1437589 CCTGCTATTTGAGGACAAAGGAAAAAGGAAAT-AAA-GTACGTCCTGCTCTTTGAGGACAAAAGA
1 CCTGCTCTTTGAGGACAAAGGAAAAAAGAAATGAAATGT--GTCCTGCTCTTTGAGGACAAAAGA
* * * * * * *
1437652 GAAAAGAAGGAAATGAAGTGTGTCCTGCTCTTTGAGGACAATGTGACAATAAGAAAATGAGGTAC
64 -AAAAGAAGGAAA--AAGTGCGTCCTGCTCTTTGAGGACAAAGAGAAAAGAAGGAAATGAGGTGC
*
1437717 GC
126 AC
* * * *
1437719 CCTGCTCTTTGAGGACAAAGGAAAAAAAAAATGAAATGTGCCCTACTCTTTGTA-GACAAATGAA
1 CCTGCTCTTTGAGGACAAAGGAAAAAAGAAATGAAATGTGTCCTGCTCTTTG-AGGACAAAAGAA
** * *
1437783 AAATGAAAAAAAAAAAGTGCGTCCTGTTCTTTGAGGACAAAAGAGAAAAGAAGGAAATGAAGTGC
65 AAA-G--AAGGAAAAAGTGCGTCCTGCTCTTTGAGGAC-AAAGAGAAAAGAAGGAAATGAGGTGC
*
1437848 AT
126 AC
* *
1437850 CCTACTCTTTGAGGACAAAAGGACAAGAAAGAAATGAAATGTGTCCTGCTCTTTGAGGACAAAGG
1 CCTGCTCTTTGAGGAC-AAAGGA-AA-AAAGAAATGAAATGTGTCCTGCTCTTTGAGGACAAAAG
1437915 AGAAAAG
63 A-AAAAG
1437922 GAAAAAATGT
Statistics
Matches: 269, Mismatches: 43, Indels: 32
0.78 0.12 0.09
Matches are distributed among these distances:
121 1 0.00
122 3 0.01
123 20 0.07
124 31 0.12
125 3 0.01
126 4 0.01
127 2 0.01
129 7 0.03
130 106 0.39
131 38 0.14
132 13 0.05
133 3 0.01
134 34 0.13
135 4 0.01
ACGTcount: A:0.42, C:0.14, G:0.25, T:0.20
Consensus pattern (127 bp):
CCTGCTCTTTGAGGACAAAGGAAAAAAGAAATGAAATGTGTCCTGCTCTTTGAGGACAAAAGAAA
AAGAAGGAAAAAGTGCGTCCTGCTCTTTGAGGACAAAGAGAAAAGAAGGAAATGAGGTGCAC
Found at i:1438064 original size:124 final size:124
Alignment explanation
Indices: 1437931--1438910 Score: 1113
Period size: 124 Copynumber: 7.9 Consensus size: 124
1437921 GGAAAAAATG
* * * *
1437931 TCCTACTCTTTGAAGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCATCT
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCC
* ** *
1437996 TGCTCTTTGAGGACTAAAAGGTGTCACCAACTCATGTGGGTTTTGAAAAGAAAAAGGCA
66 TGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCA
** * * *
1438055 TCCTGCTCTTTGAGGACTAAGCGGTGCCACCAACTTGTATGGGCTTTGAAAAGAAAAAGGTGTCC
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCC
* * *
1438120 TGCTCTTTGAGGACTAGAAAGGTGCTACCAACTTGTGTGGGCTTCG-AAAGGAAAAGGCA
66 TGCTCTTTGAGGACTA-AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCA
* * * *
1438179 TCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTATGGGCTTTGAAAAGAAAAAGGTGTCC
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCC
* * *
1438244 TGCTCTTTGAGGACTAAAGGGTGCCACCAGCTTGTGTGGGCTTTGAAAAGAAAAAAGACA
66 TGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAG-AAAAAGGCA
* * * * *
1438304 GTCTTGCTCTTTGAGGACTAAAAAAGTGCCACCAGCTCGTGTGGGCTTTAAAAAGAAAAAGGCAT
1 -TCCTGCTCTTTGAGGACT-AAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGT
* * * * * *
1438369 CCTGCTCTTTGAGGACTAAAAGGTACCACTAA-TTCAGTGTAGGC-TTAAAAAGAAAAAGACG
64 CCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTT--GTGTGGGCTTTGAAAAGAAAAAGGCA
* ** * * *
1438430 TCCTGCTTTTTGAAAACTCATAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAAGGCGTCC
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCC
* * *
1438494 TGCTCTTTGAGTACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAAGGCG
66 TGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCA
* * * * * *
1438552 TCCTGCTTTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGAAAAGACGTCC
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCC
** * *
1438616 TGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGGCG
66 TGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCA
* ** * * *
1438674 TCCTGCTCTTTGAGGATTGGAAGGTGCCACCAGCTCATGTGAGCTTT-AAAAGAAAAA---GTCC
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCC
* * ** * * *
1438735 TGCTCTTTGAGAACTAAAAAGGTGCCACCAGCTCATATGGGCTTTAGAAAAAAAAAAAAGACA
66 TGCTCTTTGAGGACT-AAAAGGTGCCACCAACTTGTGTGGGCTTT-G--AAAAGAAAAAGGCA
* * * *
1438798 TCCTTCTCTTTGAGGACTAAAAGGTGCCACCAACTCGCGTGGGC-TTGAAAAGAAAAAGGCATCA
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCC
* * * *
1438862 TGCTTTTTGAGGACTCAAGGGTGCCACCAACTTGTATGGGCTTT-AAAAG
66 TGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAG
1438911 GAAATCGACG
Statistics
Matches: 734, Mismatches: 104, Indels: 38
0.84 0.12 0.04
Matches are distributed among these distances:
119 18 0.02
120 23 0.03
122 184 0.25
123 71 0.10
124 249 0.34
125 44 0.06
126 51 0.07
127 87 0.12
128 7 0.01
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.25
Consensus pattern (124 bp):
TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCC
TGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCA
Found at i:1438235 original size:61 final size:62
Alignment explanation
Indices: 1437931--1438910 Score: 1104
Period size: 61 Copynumber: 15.9 Consensus size: 62
1437921 GGAAAAAATG
* * *
1437931 TCCTACTCTTTGAAGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCA
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCA
* * ** *
1437993 TCTTGCTCTTTGAGGACTAAAAGGTGTCACCAACTCATGTGGGTTTTGAAAAGAAAAAGGCA
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCA
** * **
1438055 TCCTGCTCTTTGAGGACTAAGCGGTGCCACCAACTTGTATGGGCTTTGAAAAGAAAAAGGTG
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCA
* * *
1438117 TCCTGCTCTTTGAGGACTAGAAAGGTGCTACCAACTTGTGTGGGCTTCG-AAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACTA-AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCA
* * **
1438179 TCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTATGGGCTTTGAAAAGAAAAAGGTG
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCA
* * *
1438241 TCCTGCTCTTTGAGGACTAAAGGGTGCCACCAGCTTGTGTGGGCTTTGAAAAGAAAAAAGACA
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAG-AAAAAGGCA
* * * * *
1438304 GTCTTGCTCTTTGAGGACTAAAAAAGTGCCACCAGCTCGTGTGGGCTTTAAAAAGAAAAAGGCA
1 -TCCTGCTCTTTGAGGACT-AAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCA
* * * * * *
1438368 TCCTGCTCTTTGAGGACTAAAAGGTACCACTAA-TTCAGTGTAGGC-TTAAAAAGAAAAAGACG
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTT--GTGTGGGCTTTGAAAAGAAAAAGGCA
* ** * * *
1438430 TCCTGCTTTTTGAAAACTCATAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAAGGCG
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCA
* * *
1438491 TCCTGCTCTTTGAGTACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAAGGCG
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCA
* * * * * *
1438552 TCCTGCTTTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGAAAAGACG
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCA
** * *
1438613 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGGCG
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCA
* ** * ** *
1438674 TCCTGCTCTTTGAGGATTGGAAGGTGCCACCAGCTCATGTGAGCTTT-AAAAGAAAAA-G--
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCA
* * ** * * *
1438732 TCCTGCTCTTTGAGAACTAAAAAGGTGCCACCAGCTCATATGGGCTTTAGAAAAAAAAAAAAGAC
1 TCCTGCTCTTTGAGGACT-AAAAGGTGCCACCAACTTGTGTGGGCTTT-G--AAAAGAAAAAGGC
1438797 A
62 A
* * *
1438798 TCCTTCTCTTTGAGGACTAAAAGGTGCCACCAACTCGCGTGGGC-TTGAAAAGAAAAAGGCA
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCA
* * * * *
1438859 TCATGCTTTTTGAGGACTCAAGGGTGCCACCAACTTGTATGGGCTTT-AAAAG
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAG
1438911 GAAATCGACG
Statistics
Matches: 796, Mismatches: 104, Indels: 37
0.85 0.11 0.04
Matches are distributed among these distances:
58 16 0.02
59 25 0.03
60 1 0.00
61 319 0.40
62 273 0.34
63 66 0.08
64 27 0.03
65 53 0.07
66 16 0.02
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.25
Consensus pattern (62 bp):
TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCA
Found at i:1439167 original size:79 final size:79
Alignment explanation
Indices: 1438937--1439170 Score: 290
Period size: 79 Copynumber: 3.0 Consensus size: 79
1438927 AAATAAAATT
* * * *
1438937 GGGGTTGGAGTATCCCCTTGAAAATAATGGGGTTGGAGTATCCCCGATTGTGAAAAATCGAAGCT
1 GGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCAATTGTGAAAAATCGATGTT
*
1439002 TTAGAAATAAGGCC
66 TTAGAAATAAAGCC
*** * *
1439016 GGGGTTGGAGTATCCCCGCCAAAATAACGGGGTTGGAGTATCCCCAATTGT-AAGAAATCAATAT
1 GGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCAATTGTGAA-AAATCGATGT
1439080 TTTAGAAATAAAGCC
65 TTTAGAAATAAAGCC
* * ** * * *
1439095 GGGGTTGGAGTATCCCCTTGGAAATAACGGGATTGGAGTATCCATAATTATGAAAATTTGATGTT
1 GGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCAATTGTGAAAAATCGATGTT
*
1439160 TTGGAAATAAA
66 TTAGAAATAAA
1439171 ATTGGAGTTA
Statistics
Matches: 130, Mismatches: 23, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
78 2 0.02
79 126 0.97
80 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.27
Consensus pattern (79 bp):
GGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCAATTGTGAAAAATCGATGTT
TTAGAAATAAAGCC
Found at i:1441578 original size:20 final size:20
Alignment explanation
Indices: 1441553--1441602 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1441543 TGCCTAAATG
1441553 TATCGATACAATGAACAATA
1 TATCGATACAATGAACAATA
* * *
1441573 TATCGATATAGTGAACAATG
1 TATCGATACAATGAACAATA
1441593 TATCGATACA
1 TATCGATACA
1441603 TCTAGGTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (20 bp):
TATCGATACAATGAACAATA
Found at i:1454890 original size:19 final size:20
Alignment explanation
Indices: 1454860--1454897 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1454850 TTGTTGAAAT
*
1454860 TATAATATTATTTTTATATA
1 TATAATATTATTATTATATA
1454880 TATAA-ATTATTATTATAT
1 TATAATATTATTATTATAT
1454898 TAAAATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TATAATATTATTATTATATA
Found at i:1455430 original size:16 final size:16
Alignment explanation
Indices: 1455407--1455469 Score: 74
Period size: 16 Copynumber: 3.9 Consensus size: 16
1455397 GCTATGATGG
1455407 ACTTTAAATTTTTTTA
1 ACTTTAAATTTTTTTA
* *
1455423 ATTTTAAATTTTTTTG
1 ACTTTAAATTTTTTTA
* *
1455439 AGTTT-AATTTTTTAAA
1 ACTTTAAATTTTTT-TA
1455455 ACTTTAAATTTTTTT
1 ACTTTAAATTTTTTT
1455470 GATAAATTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
15 8 0.21
16 22 0.58
17 8 0.21
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.63
Consensus pattern (16 bp):
ACTTTAAATTTTTTTA
Found at i:1455451 original size:32 final size:32
Alignment explanation
Indices: 1455409--1455471 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
1455399 TATGATGGAC
** *
1455409 TTTAAATTTTTTTAATTTTAAATTTTTTTGAG
1 TTTAAATTTTTAAAACTTTAAATTTTTTTGAG
*
1455441 TTTAATTTTTTAAAACTTTAAATTTTTTTGA
1 TTTAAATTTTTAAAACTTTAAATTTTTTTGA
1455472 TAAATTTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (32 bp):
TTTAAATTTTTAAAACTTTAAATTTTTTTGAG
Found at i:1455798 original size:12 final size:13
Alignment explanation
Indices: 1455774--1455803 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1455764 TTTGCTTAAA
1455774 TTGGAAGCACTTT
1 TTGGAAGCACTTT
1455787 TTGGAA-CACTTT
1 TTGGAAGCACTTT
1455799 TTGGA
1 TTGGA
1455804 GATAGAGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.40
Consensus pattern (13 bp):
TTGGAAGCACTTT
Found at i:1456324 original size:22 final size:22
Alignment explanation
Indices: 1456296--1456338 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1456286 TATTTATATC
* *
1456296 AAAAATTAACTTAATTAATTTA
1 AAAAATTAAATTAATCAATTTA
1456318 AAAAATTAAATTAATCAATTT
1 AAAAATTAAATTAATCAATTT
1456339 TAAAGGTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAAATTAAATTAATCAATTTA
Found at i:1457001 original size:16 final size:16
Alignment explanation
Indices: 1456980--1457013 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1456970 TTTGAGTTTA
*
1456980 TTCGGGCTTAAACCTT
1 TTCGGGCTCAAACCTT
*
1456996 TTCGGGCTCAAGCCTT
1 TTCGGGCTCAAACCTT
1457012 TT
1 TT
1457014 TGTATTCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.26, G:0.21, T:0.38
Consensus pattern (16 bp):
TTCGGGCTCAAACCTT
Found at i:1458968 original size:12 final size:12
Alignment explanation
Indices: 1458953--1458978 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1458943 ACTTAATAGC
1458953 ATTTATAATTGA
1 ATTTATAATTGA
1458965 ATTTATAATTGA
1 ATTTATAATTGA
1458977 AT
1 AT
1458979 CGACCGAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
ATTTATAATTGA
Found at i:1459899 original size:22 final size:21
Alignment explanation
Indices: 1459865--1459907 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
1459855 AAATCACTTT
1459865 GATAAATTATACAAAATATAA
1 GATAAATTATACAAAATATAA
*
1459886 GATAAATTTATACACAATATAA
1 GATAAA-TTATACAAAATATAA
1459908 ATATACCATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.58, C:0.07, G:0.05, T:0.30
Consensus pattern (21 bp):
GATAAATTATACAAAATATAA
Found at i:1464959 original size:116 final size:116
Alignment explanation
Indices: 1464755--1464990 Score: 391
Period size: 116 Copynumber: 2.0 Consensus size: 116
1464745 ATTTATAAAA
* * *
1464755 TCAAACAACCTTAACTATGTTTTTAAATTGAAAATGCACTTTATAAGCTTAAATAAGTACATCGA
1 TCAAACAACCTTAACTATATTTCTAAATTAAAAATGCACTTTATAAGCTTAAATAAGTACATCGA
* *
1464820 GCTTGGTATTAGAAGTTAAGCTATTTTTTGTTGGCAAATTGTTTCACCAAT
66 GCTTGGTATTAGAAGGTAAGCTATTTTTTGTTGGCAAATGGTTTCACCAAT
*
1464871 TCAAACAACCTTAACTATATTTCTAAATTAAAAATGCATTTTATAAGCTTAAATAAGTACATCGA
1 TCAAACAACCTTAACTATATTTCTAAATTAAAAATGCACTTTATAAGCTTAAATAAGTACATCGA
* * *
1464936 GCTTGGTATTATAAGGTAAGCTATTTTTTTTTGGCGAATGGTTTCACCAAT
66 GCTTGGTATTAGAAGGTAAGCTATTTTTTGTTGGCAAATGGTTTCACCAAT
1464987 TCAA
1 TCAA
1464991 TTTTCTATGC
Statistics
Matches: 111, Mismatches: 9, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
116 111 1.00
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (116 bp):
TCAAACAACCTTAACTATATTTCTAAATTAAAAATGCACTTTATAAGCTTAAATAAGTACATCGA
GCTTGGTATTAGAAGGTAAGCTATTTTTTGTTGGCAAATGGTTTCACCAAT
Found at i:1466657 original size:82 final size:82
Alignment explanation
Indices: 1466506--1466657 Score: 189
Period size: 82 Copynumber: 1.9 Consensus size: 82
1466496 TGACATGTTT
* * * * * * *
1466506 TAAGAAAATATGGATAAACTTGTCTTAACAAGACAATATCTATAGTAGACATATCTTAATATAAA
1 TAAGAAAATATGGATAAACTTGTCTCAACAAGACAATATCTAAAGCAAACAGATCTTAAGACAAA
1466571 TTGTCTTGATGTCTTAA
66 TTGTCTTGATGTCTTAA
* * *
1466588 TAAGATAATATGGATAAGCTTGTCTCAATAAGACAATATCTAAAGCAAACAAGAT-TTAAGACAA
1 TAAGAAAATATGGATAAACTTGTCTCAACAAGACAATATCTAAAGCAAAC-AGATCTTAAGACAA
*
1466652 GTTGTC
65 ATTGTC
1466658 GTGACTAAAT
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
82 55 0.95
83 3 0.05
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.32
Consensus pattern (82 bp):
TAAGAAAATATGGATAAACTTGTCTCAACAAGACAATATCTAAAGCAAACAGATCTTAAGACAAA
TTGTCTTGATGTCTTAA
Found at i:1476908 original size:2 final size:2
Alignment explanation
Indices: 1476901--1476925 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1476891 CCGTACACAA
1476901 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
1476926 TTTTTGGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1477966 original size:19 final size:18
Alignment explanation
Indices: 1477942--1477993 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
1477932 TTTTTCTCTG
1477942 CTTTTAAAAATATTTTAAC
1 CTTTTAAAAATATTTT-AC
* *
1477961 CTTTTACATAA-ATTTTAT
1 CTTTTA-AAAATATTTTAC
*
1477979 TTTTTAAAAATATTT
1 CTTTTAAAAATATTT
1477994 AATTTATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
17 3 0.11
18 10 0.37
19 11 0.41
20 3 0.11
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (18 bp):
CTTTTAAAAATATTTTAC
Found at i:1477993 original size:18 final size:18
Alignment explanation
Indices: 1477943--1478004 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
1477933 TTTTCTCTGC
**
1477943 TTTTAAAAATATTTTAACC
1 TTTTAAAAATATTTT-ATT
*
1477962 TTTTACATAA-ATTTTATT
1 TTTTA-AAAATATTTTATT
*
1477980 TTTTAAAAATATTTAATT
1 TTTTAAAAATATTTTATT
*
1477998 TATTAAA
1 TTTTAAA
1478005 TATAAATTTG
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
17 3 0.09
18 19 0.54
19 10 0.29
20 3 0.09
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTTAAAAATATTTTATT
Found at i:1478423 original size:20 final size:19
Alignment explanation
Indices: 1478371--1478424 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 19
1478361 ATGATAAGAT
*
1478371 TATATATTTATAT-ATATA
1 TATATATTTATATAATTTA
*
1478389 TATATATTT-TTTAATTTA
1 TATATATTTATATAATTTA
1478407 TATATAATTTATATAATT
1 TATAT-ATTTATATAATT
1478425 AAAAAAAACC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 2 0.07
18 18 0.60
19 4 0.13
20 6 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TATATATTTATATAATTTA
Found at i:1479293 original size:15 final size:15
Alignment explanation
Indices: 1479273--1479315 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1479263 AAATATAAGG
1479273 TTATTTTATTTATTT
1 TTATTTTATTTATTT
* *
1479288 TTATTTTAATAATTT
1 TTATTTTATTTATTT
*
1479303 TT-TATTATTTATT
1 TTATTTTATTTATT
1479316 CATTTTTCAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 8 0.35
15 15 0.65
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTATTTTATTTATTT
Found at i:1479602 original size:24 final size:25
Alignment explanation
Indices: 1479542--1479602 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
1479532 ATTTTTTAAT
*
1479542 TATATAATATATTATTTATTATATATA
1 TATAT-ATA-ATTATTTATTATATAAA
* *
1479569 TTTATGTAATT-TTTATTATATAAA
1 TATATATAATTATTTATTATATAAA
1479593 TATATATAAT
1 TATATATAAT
1479603 AGCATTAACA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 20 0.69
25 3 0.10
26 2 0.07
27 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
TATATATAATTATTTATTATATAAA
Found at i:1480090 original size:48 final size:47
Alignment explanation
Indices: 1479985--1480090 Score: 115
Period size: 48 Copynumber: 2.2 Consensus size: 47
1479975 TAATATCATT
* **
1479985 TATTTTTTTTATATTTTTGATTTATTCATAATTTAACCTCAATTCAC
1 TATTTTTTTTATATTTTTAATTTATTCATAAACTAACCTCAATTCAC
* * * *
1480032 TTTTTCTTTTTATGTTTTTAATTTATTCATAACACTCACGTCAAATTCAC
1 TATTT-TTTTTATATTTTTAATTTATTCATAA-ACTAACCTC-AATTCAC
1480082 -ATTTTTTTT
1 TATTTTTTTT
1480091 TTTTAATATT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
47 4 0.08
48 29 0.60
49 8 0.17
50 7 0.15
ACGTcount: A:0.25, C:0.14, G:0.03, T:0.58
Consensus pattern (47 bp):
TATTTTTTTTATATTTTTAATTTATTCATAAACTAACCTCAATTCAC
Found at i:1485381 original size:17 final size:17
Alignment explanation
Indices: 1485359--1485396 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
1485349 ATAAGGAACG
1485359 TATTAATTTCTTTT-ATT
1 TATTAATTT-TTTTCATT
1485376 TATTAATTTTTTTCATT
1 TATTAATTTTTTTCATT
1485393 TATT
1 TATT
1485397 CTATATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTAATTTTTTTCATT
Found at i:1485636 original size:25 final size:22
Alignment explanation
Indices: 1485597--1485647 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 22
1485587 CAAATTTAAA
1485597 AAAATTATATAAAAACTA-AATT
1 AAAATTATATAAAAA-TATAATT
1485619 AAAATTATAATAACAAAATATAATT
1 AAAATTAT-AT-A-AAAATATAATT
1485644 AAAA
1 AAAA
1485648 GATTTTAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 8 0.32
23 2 0.08
24 3 0.12
25 12 0.48
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAATTATATAAAAATATAATT
Found at i:1491655 original size:18 final size:17
Alignment explanation
Indices: 1491632--1491666 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
1491622 TATATATATT
1491632 TTAAAATTTAATAAAATA
1 TTAAAATTTAA-AAAATA
1491650 TTAAAATTTAAAAAATA
1 TTAAAATTTAAAAAATA
1491667 AAATAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TTAAAATTTAAAAAATA
Found at i:1492077 original size:22 final size:22
Alignment explanation
Indices: 1492052--1492093 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1492042 CTTATTTTAC
*
1492052 TTTTTTATTTTT-AGATTGTTG
1 TTTTTTATTTTTCACATTGTTG
1492073 TTTTTTATTTTTCACATTGTT
1 TTTTTTATTTTTCACATTGTT
1492094 TTAGCCGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.14, C:0.05, G:0.10, T:0.71
Consensus pattern (22 bp):
TTTTTTATTTTTCACATTGTTG
Found at i:1492784 original size:13 final size:13
Alignment explanation
Indices: 1492745--1492786 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
1492735 AACATAACAC
1492745 AAATATAACATAA
1 AAATATAACATAA
* *
1492758 AAAAAT-A-ATTA
1 AAATATAACATAA
1492769 AAATATAACATAA
1 AAATATAACATAA
1492782 AAATA
1 AAATA
1492787 ATATTAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
11 8 0.35
12 2 0.09
13 13 0.57
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATATAACATAA
Found at i:1492786 original size:22 final size:23
Alignment explanation
Indices: 1492745--1492801 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 23
1492735 AACATAACAC
1492745 AAATATAACATAAAAAAATAAT-T
1 AAATATAACAT-AAAAAATAATAT
1492768 AAAATATAACAT-AAAAATAATAT
1 -AAATATAACATAAAAAATAATAT
*
1492791 TAATATAACAT
1 AAATATAACAT
1492802 GAATGCTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 19 0.61
23 1 0.03
24 11 0.35
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (23 bp):
AAATATAACATAAAAAATAATAT
Found at i:1492792 original size:24 final size:23
Alignment explanation
Indices: 1492745--1492801 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 23
1492735 AACATAACAC
1492745 AAATATAACATAAAAAAATAATT
1 AAATATAACATAAAAAAATAATT
1492768 AAAATATAACATAAAAATAAT-ATT
1 -AAATATAACATAAAAA-AATAATT
1492792 -AATATAACAT
1 AAATATAACAT
1492802 GAATGCTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
22 10 0.31
24 19 0.59
25 3 0.09
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (23 bp):
AAATATAACATAAAAAAATAATT
Found at i:1492908 original size:10 final size:11
Alignment explanation
Indices: 1492893--1492928 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
1492883 ACACTACTTA
1492893 AAAAATAAT-T
1 AAAAATAATAT
1492903 AAAAATTAATAT
1 AAAAA-TAATAT
1492915 AAAAATAATAT
1 AAAAATAATAT
1492926 AAA
1 AAA
1492929 CTTATCATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 5 0.21
11 13 0.54
12 6 0.25
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AAAAATAATAT
Found at i:1492941 original size:23 final size:21
Alignment explanation
Indices: 1492891--1492962 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 21
1492881 TAACACTACT
1492891 TAAAAAATAATTAAAAATTAA
1 TAAAAAATAATTAAAAATTAA
*
1492912 TATAAAAATAA-TATAAACTTATCA
1 TA-AAAAATAATTA-AAAATTA--A
*
1492936 TAAAAAAT-TTTAAAAA-TATA
1 TAAAAAATAATTAAAAATTA-A
1492956 TAAAAAA
1 TAAAAAA
1492963 CCAATCATTA
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
20 8 0.19
21 6 0.14
22 17 0.40
23 8 0.19
24 3 0.07
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (21 bp):
TAAAAAATAATTAAAAATTAA
Found at i:1494343 original size:51 final size:49
Alignment explanation
Indices: 1494259--1494400 Score: 160
Period size: 51 Copynumber: 2.8 Consensus size: 49
1494249 TATACAAATT
* *
1494259 TTAATATAATATATTTTTATTTTTTTATTTTTTAAATGATAATTGGGGA
1 TTAATATAAAATATTTTTATTTTTTTATTTTTTAAATAATAATTGGGGA
***
1494308 TTAATATAAAATATTTTTTATTTTTTTATTATTTTAAATAATAATT-CAAA
1 TTAATATAAAATA-TTTTTATTTTTTTATT-TTTTAAATAATAATTGGGGA
*
1494358 TTTAGTATAAAATATTTTTAGAATTTTTATTATTTTTTAAATA
1 -TTAATATAAAATATTTTT---ATTTTT-TTATTTTTTAAATA
1494401 TTATTCAAAT
Statistics
Matches: 80, Mismatches: 6, Indels: 10
0.83 0.06 0.10
Matches are distributed among these distances:
49 12 0.15
50 22 0.28
51 26 0.32
53 15 0.19
54 5 0.06
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.57
Consensus pattern (49 bp):
TTAATATAAAATATTTTTATTTTTTTATTTTTTAAATAATAATTGGGGA
Found at i:1494420 original size:52 final size:51
Alignment explanation
Indices: 1494264--1494420 Score: 146
Period size: 51 Copynumber: 3.1 Consensus size: 51
1494254 AAATTTTAAT
* * ***
1494264 ATAATATATTTTT-ATTTTTTTATT-TTTTAAATGATAATTGGGGA-TTA-A
1 ATAAAATATTTTTAATTTTTTTATTATTTTAAATAATAATT-CAAATTTAGA
* *
1494312 TATAAAATATTTTTTATTTTTTTATTATTTTAAATAATAATTCAAATTTAGT
1 -ATAAAATATTTTTAATTTTTTTATTATTTTAAATAATAATTCAAATTTAGA
* *
1494364 ATAAAATATTTTTAGAATTTTTATTATT-TTTTAAAT-ATTATTCAAATTTTGA
1 ATAAAATATTTTT--AATTTTT-TTATTATTTTAAATAATAATTCAAATTTAGA
1494416 ATAAA
1 ATAAA
1494421 TTGATGCAGG
Statistics
Matches: 91, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
49 12 0.13
50 12 0.13
51 30 0.33
52 18 0.20
53 14 0.15
54 5 0.05
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.55
Consensus pattern (51 bp):
ATAAAATATTTTTAATTTTTTTATTATTTTAAATAATAATTCAAATTTAGA
Found at i:1494836 original size:14 final size:13
Alignment explanation
Indices: 1494816--1494867 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
1494806 ATTTACATAA
1494816 ATATAATATAAAT
1 ATATAATATAAAT
* *
1494829 ATTATAATTTAATT
1 A-TATAATATAAAT
*
1494843 AAATAAATATAAAT
1 ATAT-AATATAAAT
1494857 CATATAATATA
1 -ATATAATATA
1494868 TTATATATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
13 3 0.10
14 24 0.80
15 3 0.10
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATAATATAAAT
Found at i:1494851 original size:28 final size:27
Alignment explanation
Indices: 1494784--1494864 Score: 85
Period size: 28 Copynumber: 2.9 Consensus size: 27
1494774 ATTCAGATAA
* * *
1494784 AATTAAATGATTAT-AATATATGATTT
1 AATTAAATAAATATAAATATATAATTT
1494810 ACA-TAAATATAATATAAATATTATAATTT
1 A-ATTAAATA-AATATAAATA-TATAATTT
1494839 AATTAAATAAATATAAATCATATAAT
1 AATTAAATAAATATAAAT-ATATAAT
1494865 ATATTATATA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
26 6 0.13
27 5 0.11
28 20 0.43
29 15 0.33
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (27 bp):
AATTAAATAAATATAAATATATAATTT
Found at i:1497329 original size:17 final size:19
Alignment explanation
Indices: 1497299--1497339 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
1497289 ATTATATTTT
1497299 TATTTAAAATTTTA-ATA-
1 TATTTAAAATTTTATATAG
1497316 TATTTAATAA-TTTATATAG
1 TATTTAA-AATTTTATATAG
1497335 TATTT
1 TATTT
1497340 TTATTTAGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 11 0.52
18 5 0.24
19 5 0.24
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
TATTTAAAATTTTATATAG
Found at i:1498437 original size:2 final size:2
Alignment explanation
Indices: 1498430--1498454 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1498420 ATCCTATAAA
1498430 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1498455 CTTAGGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1500809 original size:14 final size:14
Alignment explanation
Indices: 1500775--1500810 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1500765 TGTTTCAGCC
*
1500775 GTAGCACCATCAGT
1 GTAGCATCATCAGT
1500789 GTAGCATCATCAGT
1 GTAGCATCATCAGT
1500803 GTAGCATC
1 GTAGCATC
1500811 CTTCAAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (14 bp):
GTAGCATCATCAGT
Found at i:1501562 original size:14 final size:15
Alignment explanation
Indices: 1501545--1501573 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1501535 ATACTGTTAA
1501545 AAAAATA-TTAATAT
1 AAAAATATTTAATAT
1501559 AAAAATATTTAATAT
1 AAAAATATTTAATAT
1501574 TACAACCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAAATATTTAATAT
Found at i:1501856 original size:39 final size:39
Alignment explanation
Indices: 1501782--1501865 Score: 100
Period size: 39 Copynumber: 2.2 Consensus size: 39
1501772 ATATAACTAT
*
1501782 TTTAATAATAAATATATTATAAATTATACTTTATAAAGA
1 TTTAATAATAAATATATTATAAATTATACTGTATAAAGA
* * * *
1501821 TTTAATAATAAATATTTTAT-TATTTTACTAGTATAAATA
1 TTTAATAATAAATATATTATAAATTATACT-GTATAAAGA
1501860 -TTAATA
1 TTTAATA
1501866 GGTATAATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
38 13 0.33
39 26 0.67
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (39 bp):
TTTAATAATAAATATATTATAAATTATACTGTATAAAGA
Found at i:1502000 original size:15 final size:14
Alignment explanation
Indices: 1501980--1502027 Score: 55
Period size: 15 Copynumber: 3.5 Consensus size: 14
1501970 AATATTCCTA
*
1501980 AAATATTACTATTT
1 AAATATTAATATTT
1501994 CAAATATTAATATTT
1 -AAATATTAATATTT
1502009 -AA-ATTAATATTT
1 AAATATTAATATTT
*
1502021 TAATATT
1 AAATATT
1502028 TAAGTCAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 10 0.33
13 4 0.13
14 3 0.10
15 13 0.43
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (14 bp):
AAATATTAATATTT
Found at i:1502037 original size:20 final size:20
Alignment explanation
Indices: 1502000--1502039 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1501990 ATTTCAAATA
*
1502000 TTAATATTTAAATTAATATT
1 TTAATATTTAAATCAATATT
*
1502020 TTAATATTTAAGTCAATATT
1 TTAATATTTAAATCAATATT
1502040 ATTATTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (20 bp):
TTAATATTTAAATCAATATT
Found at i:1502073 original size:17 final size:17
Alignment explanation
Indices: 1502051--1502103 Score: 67
Period size: 15 Copynumber: 3.3 Consensus size: 17
1502041 TTATTTTAAA
1502051 AATTATAAATAATATTT
1 AATTATAAATAATATTT
*
1502068 AATTAT-AATTATA-TT
1 AATTATAAATAATATTT
1502083 AA-TATAAATAATATTT
1 AATTATAAATAATATTT
*
1502099 TATTA
1 AATTA
1502104 ATTATTATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 3 0.10
15 10 0.33
16 9 0.30
17 8 0.27
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AATTATAAATAATATTT
Found at i:1502130 original size:32 final size:32
Alignment explanation
Indices: 1502057--1502145 Score: 108
Period size: 32 Copynumber: 2.8 Consensus size: 32
1502047 TAAAAATTAT
* * *
1502057 AAATAATATTTAATT-ATAATTATATTAATAT
1 AAATAATATTTTATTAATAATTATATAAATAG
*
1502088 AAATAATATTTTATTAATTATTATATAAATAG
1 AAATAATATTTTATTAATAATTATATAAATAG
* * *
1502120 GAATATTATTTTGTTAATAATTATAT
1 AAATAATATTTTATTAATAATTATAT
1502146 TAGTTTAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 14 0.29
32 35 0.71
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.49
Consensus pattern (32 bp):
AAATAATATTTTATTAATAATTATATAAATAG
Found at i:1503615 original size:15 final size:16
Alignment explanation
Indices: 1503595--1503624 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1503585 AATACAATAC
1503595 AATTAATA-AATATAA
1 AATTAATATAATATAA
1503610 AATTAATATAATATA
1 AATTAATATAATATA
1503625 TTAAACACGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AATTAATATAATATAA
Found at i:1503691 original size:24 final size:25
Alignment explanation
Indices: 1503664--1503715 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
1503654 TCATATTTTT
1503664 ATTTAAAATT-TAATAAATTTA-ATA
1 ATTT-AAATTATAATAAATTTACATA
* *
1503688 ATTTATATTATAATTAATTTACATA
1 ATTTAAATTATAATAAATTTACATA
1503713 ATT
1 ATT
1503716 GATATAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 4 0.17
24 14 0.58
25 6 0.25
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (25 bp):
ATTTAAATTATAATAAATTTACATA
Found at i:1503720 original size:25 final size:24
Alignment explanation
Indices: 1503674--1503720 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1503664 ATTTAAAATT
*
1503674 TAATAAATTTAATAATTTATATTA
1 TAATAAATTTAATAATTGATATTA
*
1503698 TAATTAATTTACATAATTGATAT
1 TAATAAATTTA-ATAATTGATAT
1503721 AAAAAGAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (24 bp):
TAATAAATTTAATAATTGATATTA
Found at i:1506423 original size:21 final size:22
Alignment explanation
Indices: 1506383--1506424 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1506373 TCATACTAAC
*
1506383 TTTATTTTGTGAAAAGTAATTT
1 TTTATTTTGTGAAAAATAATTT
*
1506405 TTTATTTT-TTAAAAATAATT
1 TTTATTTTGTGAAAAATAATT
1506425 ATATTTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (22 bp):
TTTATTTTGTGAAAAATAATTT
Found at i:1510699 original size:23 final size:23
Alignment explanation
Indices: 1510668--1510711 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1510658 ATTAATTAAA
**
1510668 TTTTAAATTATTGTAATTTAATT
1 TTTTAAATTATTCAAATTTAATT
*
1510691 TTTTGAATTATTCAAATTTAA
1 TTTTAAATTATTCAAATTTAA
1510712 ATTGTTGTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (23 bp):
TTTTAAATTATTCAAATTTAATT
Found at i:1510744 original size:22 final size:23
Alignment explanation
Indices: 1510700--1510747 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1510690 TTTTTGAATT
* **
1510700 ATTCAAATTTAAATTGTTGTAAA
1 ATTCAAATTAAAAGGGTTGTAAA
1510723 ATTCAAATTAAAAGGGTT-TAAA
1 ATTCAAATTAAAAGGGTTGTAAA
1510745 ATT
1 ATT
1510748 TGTCTCAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.40
Consensus pattern (23 bp):
ATTCAAATTAAAAGGGTTGTAAA
Found at i:1512109 original size:2 final size:2
Alignment explanation
Indices: 1512102--1512132 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1512092 TTTTATTGTA
1512102 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1512133 GTACATTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1512365 original size:19 final size:19
Alignment explanation
Indices: 1512343--1512379 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1512333 GTTATATTAT
*
1512343 TTAAATTTAAATATAAATA
1 TTAAATATAAATATAAATA
*
1512362 TTAAATATAATTATAAAT
1 TTAAATATAAATATAAAT
1512380 GCAATATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TTAAATATAAATATAAATA
Found at i:1512834 original size:153 final size:153
Alignment explanation
Indices: 1512624--1513079 Score: 779
Period size: 154 Copynumber: 3.0 Consensus size: 153
1512614 TTCATCGCAC
*
1512624 AACAAAAATAATTAACATGAGTGATGAGGTACCATATAAACATCAATTTCGGTCCCCCTTTCATA
1 AACAAAAATAATTAACATGAGTGATGAGGTACCATATAAACATCAATTTTGGTCCCCCTTTCATA
1512689 GTACAACAATTACCCTTTTTTTAAAAAAAAAAAATTACAGTATATTTTAGCATGCCTAACCATAA
66 GTACAACAATTACCCTTTTTTTAAAAAAAAAAAATTACAGTATATTTTAGCATGCCTAACCATAA
*
1512754 TCCCCAGAAACAAATTTTAATTA
131 TCCCCAGAAAAAAATTTTAATTA
*
1512777 AACAAAAATAATTAACATGAGTGATGAGGCACCATATAAACATCAATTTTGGTCCCCCTTTCATA
1 AACAAAAATAATTAACATGAGTGATGAGGTACCATATAAACATCAATTTTGGTCCCCCTTTCATA
*
1512842 -TACAACAATTACCCTTTTTTTTTAGAAAAAAAAAATTACAGTATATTTTAGCATGCCTAACCAT
66 GTACAACAATTACCC--TTTTTTTAAAAAAAAAAAATTACAGTATATTTTAGCATGCCTAACCAT
*
1512906 AATCACCAGAAAAAAATTTTAATTA
129 AATCCCCAGAAAAAAATTTTAATTA
*
1512931 AACAAAAAATAATTAACATGAGTGATGAGGTAACATATAAACATCAATTTTGGTCCCCCTTTCAT
1 AAC-AAAAATAATTAACATGAGTGATGAGGTACCATATAAACATCAATTTTGGTCCCCCTTTCAT
* * * * *
1512996 AGTACAACAATTTCCCTTTTTTTAAAAAAGAAAAATTGCACTATAATTTAGCATGCCTAACCATA
65 AGTACAACAATTACCCTTTTTTTAAAAAAAAAAAATTACAGTATATTTTAGCATGCCTAACCATA
1513061 ATCCCCAGAAAAAAATTTT
130 ATCCCCAGAAAAAAATTTT
1513080 TGCATTATTG
Statistics
Matches: 285, Mismatches: 14, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
152 14 0.05
153 63 0.22
154 135 0.47
155 60 0.21
156 13 0.05
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (153 bp):
AACAAAAATAATTAACATGAGTGATGAGGTACCATATAAACATCAATTTTGGTCCCCCTTTCATA
GTACAACAATTACCCTTTTTTTAAAAAAAAAAAATTACAGTATATTTTAGCATGCCTAACCATAA
TCCCCAGAAAAAAATTTTAATTA
Found at i:1513453 original size:21 final size:22
Alignment explanation
Indices: 1513419--1513467 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
1513409 AATCCAGTCA
* * * *
1513419 AAAAATTGTTTTTTCTTTTTTT
1 AAAAATTGTATTTTATATTATT
1513441 AAAAATT-TATTTTATATTATT
1 AAAAATTGTATTTTATATTATT
1513462 AAAAAT
1 AAAAAT
1513468 AATATTCAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
AAAAATTGTATTTTATATTATT
Found at i:1513516 original size:24 final size:24
Alignment explanation
Indices: 1513489--1513536 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1513479 ATATTTTTAT
1513489 ATTAAT-ATTTATAATTAATTTAAA
1 ATTAATAATTTATAATT-ATTTAAA
*
1513513 ATTAATAATTTTTAATTATTTAAA
1 ATTAATAATTTATAATTATTTAAA
1513537 TAAATGGATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
ATTAATAATTTATAATTATTTAAA
Found at i:1514642 original size:43 final size:41
Alignment explanation
Indices: 1514594--1514684 Score: 105
Period size: 43 Copynumber: 2.2 Consensus size: 41
1514584 TTTTAATATT
*
1514594 AAATTATATTATAAA-TTACCAAAATTATTTATAAAT-TTTATCA
1 AAATTATATTA-AAAGTTAACAAAATTA-TTATAAATATTT-T-A
* *
1514637 AAATTATGTTAAAAGTTAATAAAATTATTATAAATATTTTA
1 AAATTATATTAAAAGTTAACAAAATTATTATAAATATTTTA
1514678 AAATTAT
1 AAATTAT
1514685 TAAAAATTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
41 8 0.19
42 12 0.28
43 23 0.53
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (41 bp):
AAATTATATTAAAAGTTAACAAAATTATTATAAATATTTTA
Found at i:1514650 original size:11 final size:10
Alignment explanation
Indices: 1514614--1514694 Score: 53
Period size: 10 Copynumber: 7.8 Consensus size: 10
1514604 ATAAATTACC
1514614 AAAATTATTT
1 AAAATTATTT
1514624 ATAAATT-TTAT
1 A-AAATTATT-T
1514635 CAAAATTATGTT
1 -AAAATTAT-TT
*
1514647 AAAAGTTA-AT
1 AAAA-TTATTT
1514657 AAAATTA-TT
1 AAAATTATTT
1514666 ATAAA-TATTTT
1 A-AAATTA-TTT
*
1514677 AAAATTATTA
1 AAAATTATTT
1514687 AAAATTAT
1 AAAATTAT
1514695 ATCAATAATA
Statistics
Matches: 58, Mismatches: 3, Indels: 20
0.72 0.04 0.25
Matches are distributed among these distances:
9 7 0.12
10 24 0.41
11 20 0.34
12 6 0.10
13 1 0.02
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.44
Consensus pattern (10 bp):
AAAATTATTT
Found at i:1514660 original size:21 final size:22
Alignment explanation
Indices: 1514594--1514670 Score: 74
Period size: 22 Copynumber: 3.6 Consensus size: 22
1514584 TTTTAATATT
*
1514594 AAATTATATTATAAA-TT-ACCA
1 AAATTAT-TTATAAAGTTAATCA
* *
1514615 AAATTATTTATAAATTTTATCA
1 AAATTATTTATAAAGTTAATCA
1514637 AAATTATGTTA-AAAGTTAAT-A
1 AAATTAT-TTATAAAGTTAATCA
1514658 AAATTA-TTATAAA
1 AAATTATTTATAAA
1514671 TATTTTAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
19 3 0.06
20 10 0.20
21 16 0.33
22 17 0.35
23 3 0.06
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.42
Consensus pattern (22 bp):
AAATTATTTATAAAGTTAATCA
Found at i:1514728 original size:21 final size:21
Alignment explanation
Indices: 1514677--1514898 Score: 85
Period size: 21 Copynumber: 10.4 Consensus size: 21
1514667 TAAATATTTT
1514677 AAAATTATTAAAAATTATATCA
1 AAAATTA-TAAAAATTATATCA
* *
1514699 ATAATATTACT-AAAATTATCTCC
1 A-AA-ATTA-TAAAAATTATATCA
* *
1514722 AAAATTATCAAAATTATAATAA
1 AAAATTATAAAAATTAT-ATCA
** **
1514744 AAAAGAATCAAAAAATTATATTG
1 AAAATTAT--AAAAATTATATCA
* * *
1514767 AAGATTATTAAAGTTATAT-A
1 AAAATTATAAAAATTATATCA
* * * *
1514787 AAATAATATCAATATTATATAA
1 AAA-ATTATAAAAATTATATCA
*
1514809 AAAATTA-ATAAAATCATATCA
1 AAAATTATA-AAAATTATATCA
* *
1514830 AAAA-TATCAAAATTATAT-T
1 AAAATTATAAAAATTATATCA
* **
1514849 AATATTACCAAAATTATATCA
1 AAAATTATAAAAATTATATCA
* * * * *
1514870 CATATTATTAAGACTATATCA
1 AAAATTATAAAAATTATATCA
*
1514891 AAATTTAT
1 AAAATTAT
1514899 CAAATGAATT
Statistics
Matches: 147, Mismatches: 41, Indels: 25
0.69 0.19 0.12
Matches are distributed among these distances:
19 3 0.02
20 27 0.18
21 70 0.48
22 14 0.10
23 20 0.14
24 13 0.09
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.35
Consensus pattern (21 bp):
AAAATTATAAAAATTATATCA
Found at i:1515330 original size:21 final size:22
Alignment explanation
Indices: 1515244--1515469 Score: 94
Period size: 21 Copynumber: 10.9 Consensus size: 22
1515234 TAATTGTTAC
*
1515244 AAAGGTTAT-TAAATTATA-TA
1 AAAGGTTATCAAAATTATATTA
** *
1515264 AAATATTATCAAAACTATATT-
1 AAAGGTTATCAAAATTATATTA
* *
1515285 AAGGGTTATCAAAATTAT-TACA
1 AAAGGTTATCAAAATTATAT-TA
*
1515307 AAAGGTTAT-TAAATTATATTA
1 AAAGGTTATCAAAATTATATTA
** * *
1515328 AAAATTATATCAAAAGT-TATCA
1 AAAGGT-TATCAAAATTATATTA
1515350 AAA---T-T-AAAATTATATTA
1 AAAGGTTATCAAAATTATATTA
* *
1515367 AAA-ATTAAT-AAAATCATA-TA
1 AAAGGTT-ATCAAAATTATATTA
* *
1515387 AAGGGTTATCAAAACTATATTA
1 AAAGGTTATCAAAATTATATTA
* *
1515409 AATA--TTGTTAAAATTATATT-
1 AA-AGGTTATCAAAATTATATTA
* *
1515429 AAAGGCTAGT-AAAAATATATTA
1 AAAGGTTA-TCAAAATTATATTA
*
1515451 AAA-GTTATCAAAATCATAT
1 AAAGGTTATCAAAATTATAT
1515470 CAAAGGACAT
Statistics
Matches: 151, Mismatches: 34, Indels: 41
0.67 0.15 0.18
Matches are distributed among these distances:
16 5 0.03
17 8 0.05
18 1 0.01
19 2 0.01
20 17 0.11
21 86 0.57
22 28 0.19
23 4 0.03
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.36
Consensus pattern (22 bp):
AAAGGTTATCAAAATTATATTA
Found at i:1515334 original size:12 final size:12
Alignment explanation
Indices: 1515317--1515373 Score: 53
Period size: 12 Copynumber: 4.5 Consensus size: 12
1515307 AAAGGTTATT
1515317 AAATTATATTAA
1 AAATTATATTAA
*
1515329 AAATTATATCAA
1 AAATTATATTAA
*
1515341 AAGTTATCAAAATT-A
1 AAATTAT----ATTAA
1515356 AAATTATATTAA
1 AAATTATATTAA
1515368 AAATTA
1 AAATTA
1515374 ATAAAATCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
11 3 0.08
12 24 0.67
15 7 0.19
16 2 0.06
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.37
Consensus pattern (12 bp):
AAATTATATTAA
Found at i:1515421 original size:42 final size:41
Alignment explanation
Indices: 1515354--1515475 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
1515344 TTATCAAAAT
* * *
1515354 TAAAATTATATTAAAAATTAATAAAATCATATAAAGGGTTA-
1 TAAAAATATATT-AAAATTATTAAAATCATATAAAGGGCTAG
* * *
1515395 TCAAAACTATATTAAATATTGTTAAAATTATATTAAA-GGCTAG
1 T-AAAAATATATTAAA-ATTATTAAAATCATA-TAAAGGGCTAG
*
1515438 TAAAAATATATTAAAAGTTATCAAAATCATATCAAAGG
1 TAAAAATATATTAAAA-TTATTAAAATCATAT-AAAGG
1515476 ACATAAGTAA
Statistics
Matches: 65, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
41 6 0.09
42 53 0.82
43 6 0.09
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (41 bp):
TAAAAATATATTAAAATTATTAAAATCATATAAAGGGCTAG
Found at i:1516065 original size:23 final size:20
Alignment explanation
Indices: 1515922--1516128 Score: 152
Period size: 21 Copynumber: 10.1 Consensus size: 20
1515912 ATATTCAAGA
1515922 TTATCAAAATTATATCAAAAG
1 TTATCAAAATTATAT-AAAAG
* *
1515943 -TATCAAAACTATATTAAAG
1 TTATCAAAATTATATAAAAG
* * *
1515962 CTATCCTAAA-TATAAAGAAAG
1 TTAT-CAAAATTATATA-AAAG
* * *
1515983 CTA-CAAAAATATATCAAAG
1 TTATCAAAATTATATAAAAG
1516002 TTTATCAAAATTATATAAAAG
1 -TTATCAAAATTATATAAAAG
*
1516023 TTACCAAAATTATATTAAAAG
1 TTATCAAAATTATA-TAAAAG
1516044 TTAAATCAAAATTATATAAAAAG
1 TT--ATCAAAATTATAT-AAAAG
* * * *
1516067 TGATTATAATTATATAATA-
1 TTATCAAAATTATATAAAAG
* *
1516086 TTATCAAAGTTATATTAAAAA
1 TTATCAAAATTATA-TAAAAG
* *
1516107 CTATCAAAATTATATCAAAG
1 TTATCAAAATTATATAAAAG
1516127 TT
1 TT
1516129 GCCAAAAGAG
Statistics
Matches: 147, Mismatches: 27, Indels: 25
0.74 0.14 0.13
Matches are distributed among these distances:
19 22 0.15
20 51 0.35
21 56 0.38
22 1 0.01
23 17 0.12
ACGTcount: A:0.53, C:0.09, G:0.05, T:0.33
Consensus pattern (20 bp):
TTATCAAAATTATATAAAAG
Found at i:1516124 original size:11 final size:11
Alignment explanation
Indices: 1515986--1516125 Score: 75
Period size: 11 Copynumber: 13.4 Consensus size: 11
1515976 AAGAAAGCTA
*
1515986 CAAAAATATAT
1 CAAAATTATAT
*
1515997 CAAAGTT-TAT
1 CAAAATTATAT
1516007 CAAAATTATAT
1 CAAAATTATAT
* *
1516018 -AAAAGT-TAC
1 CAAAATTATAT
1516027 CAAAATTATAT
1 CAAAATTATAT
* *
1516038 TAAAAGTTAAAT
1 CAAAA-TTATAT
1516050 CAAAATTATAT
1 CAAAATTATAT
* *
1516061 AAAAAGTGAT-T
1 CAAAA-TTATAT
*
1516072 -ATAATTATAT
1 CAAAATTATAT
*
1516082 -AATA-T-TAT
1 CAAAATTATAT
*
1516090 CAAAGTTATAT
1 CAAAATTATAT
*
1516101 TAAAA--ACTAT
1 CAAAATTA-TAT
1516111 CAAAATTATAT
1 CAAAATTATAT
1516122 CAAA
1 CAAA
1516126 GTTGCCAAAA
Statistics
Matches: 95, Mismatches: 22, Indels: 24
0.67 0.16 0.17
Matches are distributed among these distances:
8 3 0.03
9 9 0.09
10 33 0.35
11 37 0.39
12 13 0.14
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.34
Consensus pattern (11 bp):
CAAAATTATAT
Found at i:1516391 original size:21 final size:21
Alignment explanation
Indices: 1516344--1516413 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
1516334 ATCAAAATTA
* * *
1516344 TATTAAAA-ATCATCAAAAGT
1 TATTAAAATAACATTAAAAGC
* * *
1516364 TACTAAAATCATATTAAAAGC
1 TATTAAAATAACATTAAAAGC
1516385 TATTAAAATAACATTAAAAGC
1 TATTAAAATAACATTAAAAGC
1516406 TATTAAAA
1 TATTAAAA
1516414 CTATATCAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
20 7 0.17
21 33 0.82
ACGTcount: A:0.56, C:0.10, G:0.04, T:0.30
Consensus pattern (21 bp):
TATTAAAATAACATTAAAAGC
Found at i:1516424 original size:21 final size:21
Alignment explanation
Indices: 1516355--1516424 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
1516345 ATTAAAAATC
* * *
1516355 ATCAAAAGTTACTAAAATCAT
1 ATCAAAAGCTATTAAAATAAT
* *
1516376 ATTAAAAGCTATTAAAATAAC
1 ATCAAAAGCTATTAAAATAAT
*
1516397 ATTAAAAGCTATTAAAACT-AT
1 ATCAAAAGCTATTAAAA-TAAT
1516418 ATCAAAA
1 ATCAAAA
1516425 TTATATTTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
21 40 0.98
22 1 0.02
ACGTcount: A:0.56, C:0.11, G:0.04, T:0.29
Consensus pattern (21 bp):
ATCAAAAGCTATTAAAATAAT
Found at i:1517160 original size:2 final size:2
Alignment explanation
Indices: 1517153--1517177 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1517143 TTTGATTCAC
1517153 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1517178 GCAAAAGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1526165 original size:24 final size:28
Alignment explanation
Indices: 1526110--1526166 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
1526100 AAGGCTTATT
1526110 TATTATTTAATTATAATTTAAATTAATAA
1 TATTATTTAATTATAATTT-AATTAATAA
1526139 TATTATTTAATT-T-ATTT-A-TAATAA
1 TATTATTTAATTATAATTTAATTAATAA
1526163 TATT
1 TATT
1526167 TTATTTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
24 10 0.36
25 1 0.04
27 4 0.14
28 1 0.04
29 12 0.43
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
TATTATTTAATTATAATTTAATTAATAA
Found at i:1526932 original size:19 final size:18
Alignment explanation
Indices: 1526905--1526944 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1526895 ATTTATAATA
1526905 ATATAAAAATATAATTTTT
1 ATATAAAAAT-TAATTTTT
* *
1526924 ATATTAAAATTTATTTTT
1 ATATAAAAATTAATTTTT
1526942 ATA
1 ATA
1526945 AATAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATAAAAATTAATTTTT
Found at i:1527506 original size:2 final size:2
Alignment explanation
Indices: 1527499--1527531 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1527489 TGCAGTTGTA
1527499 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1527532 ATATATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1527536 original size:2 final size:2
Alignment explanation
Indices: 1527531--1527559 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1527521 TCTCTCTCTC
1527531 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1527560 GAGTTTCAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1532647 original size:13 final size:13
Alignment explanation
Indices: 1532618--1532646 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1532608 ACTCAATAAC
1532618 AAAAGAAAAAAAG
1 AAAAGAAAAAAAG
1532631 AAAAG-AAAAAAG
1 AAAAGAAAAAAAG
1532643 AAAA
1 AAAA
1532647 AAAGGGTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAAAG
Found at i:1533708 original size:19 final size:18
Alignment explanation
Indices: 1533684--1533722 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1533674 ATTTCAAAAA
* *
1533684 TATTTATTATTCATAGTAT
1 TATTTACTATT-ATAATAT
1533703 TATTTACTATTATAATAT
1 TATTTACTATTATAATAT
1533721 TA
1 TA
1533723 AAATAGTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (18 bp):
TATTTACTATTATAATAT
Found at i:1534116 original size:14 final size:16
Alignment explanation
Indices: 1534097--1534133 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
1534087 TATTTTTAAT
1534097 AATTTAAT-TAAT-TA
1 AATTTAATATAATATA
1534111 AATTTAATATAATATA
1 AATTTAATATAATATA
*
1534127 TATTTAA
1 AATTTAA
1534134 GAACTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 8 0.40
15 4 0.20
16 8 0.40
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AATTTAATATAATATA
Found at i:1534699 original size:2 final size:2
Alignment explanation
Indices: 1534694--1534734 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1534684 TCTCCCTAGG
1534694 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1534735 AGTTAGAAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1536118 original size:24 final size:25
Alignment explanation
Indices: 1536090--1536159 Score: 90
Period size: 24 Copynumber: 2.8 Consensus size: 25
1536080 AATAAAAATT
*
1536090 AGCCACCAATTTTGACAAA-CAACA
1 AGCCACCAATTTTGACAAATAAACA
1536114 AGCCACCAATTTTGACAAATAAACA
1 AGCCACCAATTTTGACAAATAAACA
**
1536139 AGCCTTC-ATATTTGACAAATA
1 AGCCACCAAT-TTTGACAAATA
1536160 CAAAGGAAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
24 21 0.51
25 20 0.49
ACGTcount: A:0.44, C:0.24, G:0.09, T:0.23
Consensus pattern (25 bp):
AGCCACCAATTTTGACAAATAAACA
Found at i:1536205 original size:27 final size:27
Alignment explanation
Indices: 1536149--1536214 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 27
1536139 AGCCTTCATA
*
1536149 TTTGACAAATACAAAGGAAACCACCATT
1 TTTGACAAACACAAA-GAAACCACCATT
1536177 TTTGACAAACACAAA-ATAACCACCATT
1 TTTGACAAACACAAAGA-AACCACCATT
1536204 TTTGACAAACA
1 TTTGACAAACA
1536215 AATGGGTGGC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
26 1 0.03
27 21 0.58
28 14 0.39
ACGTcount: A:0.47, C:0.23, G:0.08, T:0.23
Consensus pattern (27 bp):
TTTGACAAACACAAAGAAACCACCATT
Found at i:1536217 original size:24 final size:24
Alignment explanation
Indices: 1536092--1536217 Score: 83
Period size: 24 Copynumber: 4.9 Consensus size: 24
1536082 TAAAAATTAG
* *
1536092 CCACCAATTTTGACAAACAACA-AG
1 CCACCATTTTTGACAAACAA-ATAA
* * *
1536116 CCACCAATTTTGACAAATAAACAA
1 CCACCATTTTTGACAAACAAATAA
** * *
1536140 GCCTTCATATTTGACAAATACAAAGGAAA
1 -CCACCATTTTTGAC-AA-ACAAA--TAA
1536169 CCACCATTTTTGACAAACACAAAATAA
1 CCACCATTTTTGAC-AA-AC-AAATAA
1536196 CCACCATTTTTGACAAACAAAT
1 CCACCATTTTTGACAAACAAAT
1536218 GGGTGGCTTT
Statistics
Matches: 82, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
23 1 0.01
24 24 0.29
25 12 0.15
26 4 0.05
27 20 0.24
28 16 0.20
29 5 0.06
ACGTcount: A:0.46, C:0.25, G:0.07, T:0.22
Consensus pattern (24 bp):
CCACCATTTTTGACAAACAAATAA
Found at i:1538120 original size:21 final size:22
Alignment explanation
Indices: 1538094--1538139 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
1538084 ATCTGTTGAA
* *
1538094 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGTGGAGTACT
1538115 ACTCCACCTGCTGTGGAGTACT
1 ACTCCACCTGCTGTGGAGTACT
1538137 ACT
1 ACT
1538140 TGTCTGAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.33
Consensus pattern (22 bp):
ACTCCACCTGCTGTGGAGTACT
Found at i:1540712 original size:24 final size:25
Alignment explanation
Indices: 1540684--1540753 Score: 90
Period size: 24 Copynumber: 2.8 Consensus size: 25
1540674 AATAAAAATT
*
1540684 AGCCACCAATTTTGACAAA-CAACA
1 AGCCACCAATTTTGACAAATAAACA
1540708 AGCCACCAATTTTGACAAATAAACA
1 AGCCACCAATTTTGACAAATAAACA
**
1540733 AGCCTTC-ATATTTGACAAATA
1 AGCCACCAAT-TTTGACAAATA
1540754 CAAAGGAAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
24 21 0.51
25 20 0.49
ACGTcount: A:0.44, C:0.24, G:0.09, T:0.23
Consensus pattern (25 bp):
AGCCACCAATTTTGACAAATAAACA
Found at i:1540799 original size:27 final size:27
Alignment explanation
Indices: 1540743--1540808 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 27
1540733 AGCCTTCATA
*
1540743 TTTGACAAATACAAAGGAAACCACCATT
1 TTTGACAAACACAAA-GAAACCACCATT
1540771 TTTGACAAACACAAA-ATAACCACCATT
1 TTTGACAAACACAAAGA-AACCACCATT
1540798 TTTGACAAACA
1 TTTGACAAACA
1540809 AATGGGTGGC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
26 1 0.03
27 21 0.58
28 14 0.39
ACGTcount: A:0.47, C:0.23, G:0.08, T:0.23
Consensus pattern (27 bp):
TTTGACAAACACAAAGAAACCACCATT
Found at i:1540811 original size:24 final size:24
Alignment explanation
Indices: 1540686--1540811 Score: 83
Period size: 24 Copynumber: 4.9 Consensus size: 24
1540676 TAAAAATTAG
* *
1540686 CCACCAATTTTGACAAACAACA-AG
1 CCACCATTTTTGACAAACAA-ATAA
* * *
1540710 CCACCAATTTTGACAAATAAACAA
1 CCACCATTTTTGACAAACAAATAA
** * *
1540734 GCCTTCATATTTGACAAATACAAAGGAAA
1 -CCACCATTTTTGAC-AA-ACAAA--TAA
1540763 CCACCATTTTTGACAAACACAAAATAA
1 CCACCATTTTTGAC-AA-AC-AAATAA
1540790 CCACCATTTTTGACAAACAAAT
1 CCACCATTTTTGACAAACAAAT
1540812 GGGTGGCTTT
Statistics
Matches: 82, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
23 1 0.01
24 24 0.29
25 12 0.15
26 4 0.05
27 20 0.24
28 16 0.20
29 5 0.06
ACGTcount: A:0.46, C:0.25, G:0.07, T:0.22
Consensus pattern (24 bp):
CCACCATTTTTGACAAACAAATAA
Found at i:1543054 original size:29 final size:27
Alignment explanation
Indices: 1543021--1543077 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 27
1543011 TTTACAATCG
1543021 AATTATATAATA-TTATTTATTAATAATAA
1 AATTAT-TAATATTTATTT-TTAA-AATAA
*
1543050 AATTATTTATATTTATTTTTAAAATAA
1 AATTATTAATATTTATTTTTAAAATAA
1543077 A
1 A
1543078 TTTTAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 6 0.23
28 8 0.31
29 12 0.46
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
AATTATTAATATTTATTTTTAAAATAA
Found at i:1543252 original size:11 final size:11
Alignment explanation
Indices: 1543208--1543284 Score: 56
Period size: 11 Copynumber: 7.1 Consensus size: 11
1543198 AATGTTCACC
1543208 TAATATAATTATA
1 TAATATAA--ATA
*
1543221 TAATAT-ATTA
1 TAATATAAATA
1543231 TACAGTATAAATA
1 TA-A-TATAAATA
1543244 TAATATAAA-A
1 TAATATAAATA
1543254 -AAT-T-AATA
1 TAATATAAATA
* *
1543262 AAATATAAAAA
1 TAATATAAATA
1543273 TAATATAAATA
1 TAATATAAATA
1543284 T
1 T
1543285 TTTAAATATT
Statistics
Matches: 52, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
7 2 0.04
8 2 0.04
9 6 0.12
10 6 0.12
11 20 0.38
12 5 0.10
13 11 0.21
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (11 bp):
TAATATAAATA
Found at i:1543261 original size:18 final size:16
Alignment explanation
Indices: 1543240--1543280 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 16
1543230 ATACAGTATA
1543240 AATATAATATAAAAAATT
1 AATATAATAT-AAAAA-T
*
1543258 AATAAAATATAAAAAT
1 AATATAATATAAAAAT
1543274 AATATAA
1 AATATAA
1543281 ATATTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.33
17 5 0.24
18 9 0.43
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AATATAATATAAAAAT
Found at i:1543262 original size:16 final size:16
Alignment explanation
Indices: 1543240--1543284 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 16
1543230 ATACAGTATA
*
1543240 AATATAATATAAAAAATT
1 AATAAAATAT-AAAAA-T
1543258 AATAAAATATAAAAAT
1 AATAAAATATAAAAAT
1543274 AATATAAATAT
1 AATA-AAATAT
1543285 TTTAAATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 5 0.20
17 11 0.44
18 9 0.36
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AATAAAATATAAAAAT
Found at i:1543330 original size:16 final size:17
Alignment explanation
Indices: 1543312--1543368 Score: 61
Period size: 15 Copynumber: 3.6 Consensus size: 17
1543302 ATCATAATGT
*
1543312 AAATAATATA-AATTTT
1 AAATAATATATAATTTA
1543328 AAAT-ATA-ATAATTTAA
1 AAATAATATATAATTT-A
1543344 AAATAAT-TATAA-TTA
1 AAATAATATATAATTTA
1543359 AAATAATATA
1 AAATAATATA
1543369 AATATTATCG
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 1 0.03
15 16 0.46
16 12 0.34
17 6 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATAATATATAATTTA
Found at i:1545667 original size:101 final size:101
Alignment explanation
Indices: 1545489--1545678 Score: 292
Period size: 101 Copynumber: 1.9 Consensus size: 101
1545479 TATGTGTATT
* * *
1545489 TTTATAAAATTCCACCCTTAACATAAATGTCATGAATTTGTTAAGTGACATGTTCTGTAATTGAA
1 TTTATAAAATTCCACCCTTAACAAAAATGTCATGAATTTGTTAACTGACATGTTCTGCAATTGAA
1545554 AAAAAAAATACCAAATTAAACAAATCAATTCGAGGC
66 AAAAAAAATACCAAATTAAACAAATCAATTCGAGGC
* * *
1545590 TTTATAAAATTCCACCTTTAACAAAAATGTCATGACTTTGTTAACTGACATATT-TCGCAATTGA
1 TTTATAAAATTCCACCCTTAACAAAAATGTCATGAATTTGTTAACTGACATGTTCT-GCAATTGA
* *
1545654 AAAAAATATTACCAAATTAAACAAA
65 AAAAAAAAATACCAAATTAAACAAA
1545679 ATTAATTCAA
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
100 1 0.01
101 79 0.99
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (101 bp):
TTTATAAAATTCCACCCTTAACAAAAATGTCATGAATTTGTTAACTGACATGTTCTGCAATTGAA
AAAAAAAATACCAAATTAAACAAATCAATTCGAGGC
Found at i:1549453 original size:2 final size:2
Alignment explanation
Indices: 1549448--1549482 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1549438 GAGATATATC
1549448 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1549483 TGCTCTTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1549757 original size:2 final size:2
Alignment explanation
Indices: 1549750--1549791 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1549740 ATCGTATTAA
1549750 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1549792 CACGTAACTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1553698 original size:2 final size:2
Alignment explanation
Indices: 1553691--1553739 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
1553681 AGAAGTTTCA
* *
1553691 TC TC TC TC TC TA TC TC TC TC TC TC TC TC TC TC TC CC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1553733 TC TC TC T
1 TC TC TC T
1553740 ATTCAAGAGT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.02, C:0.49, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:1554303 original size:24 final size:24
Alignment explanation
Indices: 1554265--1554335 Score: 69
Period size: 23 Copynumber: 3.1 Consensus size: 24
1554255 ATTATGATTT
* *
1554265 TAAATAATTAATTTATATATTTAA
1 TAAATATTTATTTTATATATTTAA
* *
1554289 TTAATATTTATTTTAT-T-TTAAA
1 TAAATATTTATTTTATATATTTAA
1554311 TAAATTATTTATTTTA-A-ATTTAA
1 TAAA-TATTTATTTTATATATTTAA
1554334 TA
1 TA
1554336 TTTTTTTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
22 7 0.18
23 18 0.47
24 13 0.34
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TAAATATTTATTTTATATATTTAA
Found at i:1554321 original size:42 final size:40
Alignment explanation
Indices: 1554261--1554345 Score: 111
Period size: 42 Copynumber: 2.1 Consensus size: 40
1554251 TAAAATTATG
*
1554261 ATTTTAAATAATTAATTTATATATTTAA-TTAATATTTATTTT
1 ATTTTAAATAATTAATTTAT-T-TTAAATTTAATATTT-TTTT
1554303 ATTTTAAATAAATT-ATTTATTTTAAATTTAATATTTTTTT
1 ATTTTAAAT-AATTAATTTATTTTAAATTTAATATTTTTTT
1554343 ATT
1 ATT
1554346 ATTTATTAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
40 11 0.28
41 10 0.25
42 15 0.38
43 4 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (40 bp):
ATTTTAAATAATTAATTTATTTTAAATTTAATATTTTTTT
Found at i:1554337 original size:18 final size:18
Alignment explanation
Indices: 1554274--1554343 Score: 60
Period size: 18 Copynumber: 4.0 Consensus size: 18
1554264 TTAAATAATT
*
1554274 AATTTATATATTTA-ATTA
1 AATTTA-ATATTTATTTTA
1554292 ATATTT-AT-TTTATTTTA
1 A-ATTTAATATTTATTTTA
*
1554309 AA-TAAATTATTTATTTTA
1 AATTTAA-TATTTATTTTA
1554327 AATTTAATATTT-TTTTA
1 AATTTAATATTTATTTTA
1554344 TTATTTATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
15 1 0.02
16 6 0.14
17 12 0.28
18 17 0.40
19 7 0.16
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
AATTTAATATTTATTTTA
Found at i:1554415 original size:15 final size:16
Alignment explanation
Indices: 1554391--1554424 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1554381 TACATACACA
1554391 TTTTAATATAATT-AT
1 TTTTAATATAATTCAT
*
1554406 TTTTACTATAATTCAT
1 TTTTAATATAATTCAT
1554422 TTT
1 TTT
1554425 ACCATCACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTAATATAATTCAT
Found at i:1554425 original size:15 final size:15
Alignment explanation
Indices: 1554389--1554426 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1554379 ATTACATACA
*
1554389 CATTTTAATATAATT
1 CATTTTACTATAATT
1554404 -ATTTTTACTATAATT
1 CA-TTTTACTATAATT
1554419 CATTTTAC
1 CATTTTAC
1554427 CATCACAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
14 1 0.05
15 18 0.90
16 1 0.05
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (15 bp):
CATTTTACTATAATT
Found at i:1554832 original size:16 final size:16
Alignment explanation
Indices: 1554798--1554831 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1554788 TAGATTTGAA
1554798 TTTAATTTTAAATTAT
1 TTTAATTTTAAATTAT
1554814 TTTAATTTTAAATT-T
1 TTTAATTTTAAATTAT
1554829 TTT
1 TTT
1554832 TGAGTTAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTAATTTTAAATTAT
Found at i:1557585 original size:25 final size:25
Alignment explanation
Indices: 1557535--1557584 Score: 93
Period size: 24 Copynumber: 2.0 Consensus size: 25
1557525 CTGCGTCCTA
1557535 TGTCCAATTTTTTAAAAATATTTTT
1 TGTCCAATTTTTTAAAAATATTTTT
1557560 TGTCC-ATTTTTTAAAAATATTTTT
1 TGTCCAATTTTTTAAAAATATTTTT
1557584 T
1 T
1557585 TAGCCGATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.30, C:0.08, G:0.04, T:0.58
Consensus pattern (25 bp):
TGTCCAATTTTTTAAAAATATTTTT
Found at i:1557895 original size:29 final size:29
Alignment explanation
Indices: 1557854--1557976 Score: 219
Period size: 29 Copynumber: 4.2 Consensus size: 29
1557844 TTAACTGTTA
* *
1557854 ATTTTTAAATAAATTATTAAAATAATATT
1 ATTTTAAAATAAATTATTAAAATATTATT
*
1557883 AATTTAAAATAAATTATTAAAATATTATT
1 ATTTTAAAATAAATTATTAAAATATTATT
1557912 ATTTTAAAATAAATTATTAAAATATTATT
1 ATTTTAAAATAAATTATTAAAATATTATT
1557941 ATTTTAAAATAAATTATTAAAATATTATT
1 ATTTTAAAATAAATTATTAAAATATTATT
1557970 ATTTTAA
1 ATTTTAA
1557977 TTAATAAAAA
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 90 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
ATTTTAAAATAAATTATTAAAATATTATT
Found at i:1557929 original size:18 final size:17
Alignment explanation
Indices: 1557870--1557976 Score: 93
Period size: 16 Copynumber: 7.2 Consensus size: 17
1557860 AAATAAATTA
*
1557870 TTAAAATAA-TATTAAT
1 TTAAAATAATTATTATT
1557886 TTAAAATAA--ATTA--
1 TTAAAATAATTATTATT
1557899 TTAAAAT-ATTATTATT
1 TTAAAATAATTATTATT
1557915 TTAAAATAA--ATTA--
1 TTAAAATAATTATTATT
1557928 TTAAAAT-ATTATTATT
1 TTAAAATAATTATTATT
1557944 TTAAAATAA--ATTA--
1 TTAAAATAATTATTATT
1557957 TTAAAAT-ATTATTATT
1 TTAAAATAATTATTATT
1557973 TTAA
1 TTAA
1557977 TTAATAAAAA
Statistics
Matches: 77, Mismatches: 0, Indels: 28
0.73 0.00 0.27
Matches are distributed among these distances:
12 3 0.04
13 21 0.27
14 12 0.16
15 12 0.16
16 27 0.35
17 2 0.03
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTAAAATAATTATTATT
Found at i:1558279 original size:19 final size:19
Alignment explanation
Indices: 1558255--1558298 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1558245 TTTTTTAAAA
*
1558255 TAATAAAAGATTATATTAT
1 TAATAAAAGATAATATTAT
1558274 TAATAAAAGATAATATTAT
1 TAATAAAAGATAATATTAT
1558293 T-ATAAA
1 TAATAAA
1558299 CATAATAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.39
Consensus pattern (19 bp):
TAATAAAAGATAATATTAT
Found at i:1558305 original size:17 final size:19
Alignment explanation
Indices: 1558255--1558305 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
1558245 TTTTTTAAAA
* *
1558255 TAATAAAAGATTATATTAT
1 TAATAAAACATAATATTAT
*
1558274 TAATAAAAGATAATATTAT
1 TAATAAAACATAATATTAT
1558293 T-AT-AAACATAATA
1 TAATAAAACATAATA
1558306 ATAATTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.30
18 2 0.07
19 19 0.63
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (19 bp):
TAATAAAACATAATATTAT
Found at i:1558402 original size:14 final size:14
Alignment explanation
Indices: 1558383--1558428 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
1558373 TCATGTTATT
1558383 ATTTAAAATATTTA
1 ATTTAAAATATTTA
** *
1558397 ATTTAATTTGTTTA
1 ATTTAAAATATTTA
1558411 ATTT-AAA-ATTTA
1 ATTTAAAATATTTA
1558423 ATTTAA
1 ATTTAA
1558429 GTTGTAATCG
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
12 8 0.32
13 2 0.08
14 15 0.60
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (14 bp):
ATTTAAAATATTTA
Found at i:1558525 original size:23 final size:22
Alignment explanation
Indices: 1558494--1558539 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
1558484 TATAATGGTT
1558494 TAATTTTTTAAAAAATTAATTA
1 TAATTTTTTAAAAAATTAATTA
**
1558516 TAATTATTTTAAAACTTTAATTA
1 TAATT-TTTTAAAAAATTAATTA
1558539 T
1 T
1558540 TTTAAATTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TAATTTTTTAAAAAATTAATTA
Found at i:1561249 original size:17 final size:17
Alignment explanation
Indices: 1561218--1561262 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
1561208 AAATATATTA
*
1561218 AATAATAAA-AAAATGC
1 AATAAAAAATAAAATGC
1561234 AATAAAAAATAAAATGC
1 AATAAAAAATAAAATGC
*
1561251 TA-AAAAAATAAA
1 AATAAAAAATAAA
1561263 TATAAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 18 0.69
17 8 0.31
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.18
Consensus pattern (17 bp):
AATAAAAAATAAAATGC
Done.