Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008128.1 Hibiscus syriacus cultivar Beakdansim tig00110683_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4987688
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 20
Found at i:2810245 original size:74 final size:73
Alignment explanation
Indices: 2810103--2810279 Score: 284
Period size: 74 Copynumber: 2.4 Consensus size: 73
2810093 GCATGAACGG
*
2810103 ATGCCATAACT-AAAATGCATGAACGGATGCCATAACTAAAATGCATGAACGAATGCATTAAGGC
1 ATGCCATAACTAAAAATGCATGAACGGATGCCATAACTAAAATACATGAACGAATGCATTAAGGC
2810167 ATGAAATA
66 ATGAAATA
* *
2810175 ATGCCATAATTAAAAATGCATGAACGGATGCCATAACTAAAAATACATGAACGAATGTATTAAGG
1 ATGCCATAACTAAAAATGCATGAACGGATGCCATAACT-AAAATACATGAACGAATGCATTAAGG
*
2810240 CATGAAATG
65 CATGAAATA
* *
2810249 ATACCATAACTAAAAATGCATAAACGGATGC
1 ATGCCATAACTAAAAATGCATGAACGGATGC
2810280 ATTAAGGCAT
Statistics
Matches: 96, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
72 10 0.10
73 26 0.27
74 60 0.62
ACGTcount: A:0.46, C:0.16, G:0.17, T:0.21
Consensus pattern (73 bp):
ATGCCATAACTAAAAATGCATGAACGGATGCCATAACTAAAATACATGAACGAATGCATTAAGGC
ATGAAATA
Found at i:2810391 original size:67 final size:67
Alignment explanation
Indices: 2810313--2810440 Score: 229
Period size: 67 Copynumber: 1.9 Consensus size: 67
2810303 AACTAAAAAT
* *
2810313 GCATGAACGGATGCATTAAGGCATGAAAGGATGCCACAACTAAAAATGCATGAACGGATGTATTA
1 GCATGAACGGATGCATTAAGGCATGAAAGAATGCCACAACTAAAAATGCATGAAAGGATGTATTA
2810378 AG
66 AG
*
2810380 GCATGAACGGATGCATTAAGGCATGAAAGAATGCCATAACTAAAAATGCATGAAAGGATGT
1 GCATGAACGGATGCATTAAGGCATGAAAGAATGCCACAACTAAAAATGCATGAAAGGATGT
2810441 TGTGTTAATA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 58 1.00
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.20
Consensus pattern (67 bp):
GCATGAACGGATGCATTAAGGCATGAAAGAATGCCACAACTAAAAATGCATGAAAGGATGTATTA
AG
Found at i:2810413 original size:20 final size:20
Alignment explanation
Indices: 2810313--2810406 Score: 89
Period size: 20 Copynumber: 4.3 Consensus size: 20
2810303 AACTAAAAAT
2810313 GCATGAACGGATGCATTAAG
1 GCATGAACGGATGCATTAAG
* * *
2810333 GCATGAAAGGATGCCACAACTAAAAAT
1 GCATGAACGGATG---C-A-T--TAAG
*
2810360 GCATGAACGGATGTATTAAG
1 GCATGAACGGATGCATTAAG
2810380 GCATGAACGGATGCATTAAG
1 GCATGAACGGATGCATTAAG
2810400 GCATGAA
1 GCATGAA
2810407 AGAATGCCAT
Statistics
Matches: 59, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
20 40 0.68
22 1 0.02
23 2 0.03
24 1 0.02
25 1 0.02
27 14 0.24
ACGTcount: A:0.39, C:0.15, G:0.27, T:0.19
Consensus pattern (20 bp):
GCATGAACGGATGCATTAAG
Found at i:2815179 original size:12 final size:13
Alignment explanation
Indices: 2815162--2815190 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2815152 GCACATCAGT
2815162 GGGAACTTCTGG-
1 GGGAACTTCTGGA
2815174 GGGAACTTCTGGA
1 GGGAACTTCTGGA
2815187 GGGA
1 GGGA
2815191 CATGTGATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.21, C:0.14, G:0.45, T:0.21
Consensus pattern (13 bp):
GGGAACTTCTGGA
Found at i:2822979 original size:17 final size:17
Alignment explanation
Indices: 2822957--2822998 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
2822947 TATAGGTGTT
2822957 GTCTATCCTACTCTAGA
1 GTCTATCCTACTCTAGA
*
2822974 GTCTATCCTACTCTAGT
1 GTCTATCCTACTCTAGA
2822991 GTCTATCC
1 GTCTATCC
2822999 CTTTTAGTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.19, C:0.31, G:0.12, T:0.38
Consensus pattern (17 bp):
GTCTATCCTACTCTAGA
Found at i:2830638 original size:2 final size:2
Alignment explanation
Indices: 2830631--2830660 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2830621 TTAGTTATTA
2830631 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
2830661 TAAATGTGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2832139 original size:2 final size:2
Alignment explanation
Indices: 2832132--2832162 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2832122 TCAATCTACA
2832132 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
2832163 ATTTACGACA
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:2832343 original size:13 final size:13
Alignment explanation
Indices: 2832327--2832399 Score: 101
Period size: 13 Copynumber: 5.6 Consensus size: 13
2832317 GCAATGAGCA
*
2832327 TCATAAATGCGTG
1 TCATAAATGCGCG
2832340 TCATAAATGCGCG
1 TCATAAATGCGCG
*
2832353 TCATAAATGCACG
1 TCATAAATGCGCG
**
2832366 TCATAAATGCATG
1 TCATAAATGCGCG
*
2832379 TCATAAATACGCG
1 TCATAAATGCGCG
2832392 TCATAAAT
1 TCATAAAT
2832400 TTATGACGCA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 54 1.00
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.27
Consensus pattern (13 bp):
TCATAAATGCGCG
Found at i:2834623 original size:19 final size:19
Alignment explanation
Indices: 2834599--2834642 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
2834589 TACCCTATAT
* *
2834599 TACTTGAATCGATTGTGTA
1 TACTTGAACCAATTGTGTA
2834618 TACTTGAACCAATTGTGTA
1 TACTTGAACCAATTGTGTA
2834637 TACTTG
1 TACTTG
2834643 CGCAGATTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (19 bp):
TACTTGAACCAATTGTGTA
Found at i:2838262 original size:15 final size:14
Alignment explanation
Indices: 2838238--2838279 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
2838228 CCTCGGTAAG
*
2838238 TTTCTCTTCTTTCTT
1 TTTCTTTTCTTTC-T
2838253 TTTCTTTTCTTTCT
1 TTTCTTTTCTTTCT
2838267 TTTCTGTTTCTTT
1 TTTCT-TTTCTTT
2838280 GCTGCGTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 6 0.24
15 19 0.76
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.76
Consensus pattern (14 bp):
TTTCTTTTCTTTCT
Found at i:2838270 original size:20 final size:20
Alignment explanation
Indices: 2838238--2838279 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2838228 CCTCGGTAAG
*
2838238 TTTCTCTTCTTTCTTTTTCT
1 TTTCTCTTCTTTCTGTTTCT
2838258 TTTCT-TTCTTTTCTGTTTCT
1 TTTCTCTTC-TTTCTGTTTCT
2838278 TT
1 TT
2838280 GCTGCGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTCTCTTCTTTCTGTTTCT
Found at i:2838366 original size:20 final size:20
Alignment explanation
Indices: 2838343--2838396 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
2838333 TCTCTCTCGG
*
2838343 TCTCTATTGTTCTCCGTCTC
1 TCTCTGTTGTTCTCCGTCTC
2838363 TCTCTGTTGTTCTCCGTCTC
1 TCTCTGTTGTTCTCCGTCTC
2838383 TCTCTGTTGTTCTC
1 TCTCTGTTGTTCTC
2838397 TTTCCTTGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.02, C:0.33, G:0.13, T:0.52
Consensus pattern (20 bp):
TCTCTGTTGTTCTCCGTCTC
Found at i:2838815 original size:3 final size:3
Alignment explanation
Indices: 2838782--2838870 Score: 106
Period size: 3 Copynumber: 28.7 Consensus size: 3
2838772 CCGGGTTTTG
* * *
2838782 TAA TAT TAA TAAA TAAA TAA TATA TAT TAA TAA TAA TAA TAA TTA TAA
1 TAA TAA TAA T-AA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
* *
2838830 TTA TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2838871 TAAATAAAAT
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
3 64 0.86
4 10 0.14
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:2839139 original size:17 final size:17
Alignment explanation
Indices: 2839117--2839172 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
2839107 TTGAATAAGC
2839117 TCTTCTCATTATGAACT
1 TCTTCTCATTATGAACT
*
2839134 TCTTCTTC-TCCTGATG-AGT
1 TCTTC-TCAT--T-ATGAACT
2839153 TCTTCTCATTATGAACT
1 TCTTCTCATTATGAACT
2839170 TCT
1 TCT
2839173 CTGGAAAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
16 3 0.10
17 12 0.39
18 4 0.13
19 9 0.29
20 3 0.10
ACGTcount: A:0.18, C:0.25, G:0.09, T:0.48
Consensus pattern (17 bp):
TCTTCTCATTATGAACT
Found at i:2839320 original size:113 final size:113
Alignment explanation
Indices: 2839100--2839763 Score: 993
Period size: 113 Copynumber: 5.9 Consensus size: 113
2839090 TAGAGTCATT
* ** * *
2839100 CAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTC-T--T-CTTCTCCTGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
* * * *
2839161 TTATGAACTTC--TCTGGAAAA-ACTGACCCATCAAGTGATGGATTTGAG
66 TTATGAAC-TCGAACTGGAAAAGA-TAATCCATCAAGTGATAGATTTGAG
* * *
2839208 CAAAA-ATCTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
1 CAAAAGGT-TGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTC
**** * * * *
2839272 ATTATGAACTTTTTCTAGAAAAGTTGATCCATCAAGTGATGGATTTGAG
65 ATTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
* *
2839321 CAAAAAGTTGAACAAATTCTTCTCATTGTGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
* *
2839386 TTATGAACTCGAACTGGAAAAGCTAATCTATCAAGTGATAGATTTGAG
66 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
*
2839434 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTGTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
*
2839499 TTACGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
66 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
*
2839547 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCGTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
*
2839612 TTATGAACTCAAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
66 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
2839660 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
2839725 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGAT
66 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGAT
2839764 GAATTTAATT
Statistics
Matches: 511, Mismatches: 36, Indels: 13
0.91 0.06 0.02
Matches are distributed among these distances:
107 1 0.00
108 30 0.06
109 1 0.00
111 2 0.00
112 28 0.05
113 448 0.88
114 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (113 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
Found at i:2840748 original size:84 final size:83
Alignment explanation
Indices: 2840493--2840962 Score: 735
Period size: 83 Copynumber: 5.6 Consensus size: 83
2840483 GGTTCCTACT
* * *
2840493 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATTCTATGAGCATATT-ACTCTTCCAAA
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCA-TCTTTCAAA
* * * * *
2840557 TTCAATGATTGGTTATGCC
65 TTCAATAACTCGTTTTACC
*
2840576 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAAT
* *
2840641 TCAATAACTTGTTTTACT
66 TCAATAACTCGTTTTACC
* *
2840659 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATTGGGCACATTCATCTTTCAAA
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCATCTTTCAAA
2840724 TTCAATAACTCGTTTTACC
65 TTCAATAACTCGTTTTACC
2840743 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAAT
* * *
2840808 TCAATGATTGGTTTTACC
66 TCAATAACTCGTTTTACC
*
2840826 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCATCTTTCAAA
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCATCTTTCAAA
2840891 TTCAATAACTCGTTTTACC
65 TTCAATAACTCGTTTTACC
* *
2840910 AAACTAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
2840963 GCATTTGTTC
Statistics
Matches: 359, Mismatches: 25, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
83 203 0.57
84 156 0.43
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (83 bp):
AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAAT
TCAATAACTCGTTTTACC
Found at i:2840773 original size:167 final size:167
Alignment explanation
Indices: 2840489--2840962 Score: 767
Period size: 167 Copynumber: 2.8 Consensus size: 167
2840479 CTGTGGTTCC
* *
2840489 TACTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT-TCTA-TGAGCATATT-ACTCT
1 TACTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGT-TATTGGGCACATTCA-TCT
* * * * * *
2840551 TCCAAATTCAATGATTGGTTATGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
64 TTCAAATTCAATAACTCGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
2840616 CTATGAGCACATTCATCTTCCAAATTCAATAACTT-GTTT
129 CTATGAGCACATTCATCTTCCAAATTCAATAA-TTGGTTT
2840655 TACTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATTGGGCACATTCATCTTT
1 TACTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATTGGGCACATTCATCTTT
2840720 CAAATTCAATAACTCGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
66 CAAATTCAATAACTCGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
* *
2840785 ATGAGCACATTCATCTTTCAAATTCAATGATTGGTTT
131 ATGAGCACATTCATCTTCCAAATTCAATAATTGGTTT
* *
2840822 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCATCTTT
1 TACTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATTGGGCACATTCATCTTT
* *
2840887 CAAATTCAATAACTCGTTTTACCAAACTAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCT
66 CAAATTCAATAACTCGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
2840952 ATGAGCACATT
131 ATGAGCACATT
2840963 GCATTTGTTC
Statistics
Matches: 290, Mismatches: 14, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
166 47 0.16
167 242 0.83
168 1 0.00
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.27
Consensus pattern (167 bp):
TACTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATTGGGCACATTCATCTTT
CAAATTCAATAACTCGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
ATGAGCACATTCATCTTCCAAATTCAATAATTGGTTT
Found at i:2842116 original size:1 final size:1
Alignment explanation
Indices: 2842110--2842198 Score: 70
Period size: 1 Copynumber: 89.0 Consensus size: 1
2842100 TGACCCCTCA
* * * * * * * * *
2842110 TTTTTTTTTCTTTCTTTTTTTCTTTTTTCTCTTTTTTCTTTTTCTTTTTTTTCTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
2842175 TTTTCTTTTTTCTTTTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTT
2842199 CTTCAAGCAT
Statistics
Matches: 64, Mismatches: 24, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 64 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (1 bp):
T
Found at i:2842130 original size:15 final size:14
Alignment explanation
Indices: 2842110--2842201 Score: 103
Period size: 15 Copynumber: 6.1 Consensus size: 14
2842100 TGACCCCTCA
*
2842110 TTTTTTTTTCTTTC
1 TTTTTTTTTTTTTC
2842124 TTTTTTTCTTTTTTC
1 TTTTTTT-TTTTTTC
*
2842139 TCTTTTTTCTTTTTC
1 T-TTTTTTTTTTTTC
2842154 TTTTTTTTCTTTTTC
1 TTTTTTTT-TTTTTC
*
2842169 TTTTTTTTTTCTTTT
1 TTTTTTTTTT-TTTC
2842184 TTCTTTTCTTTTTTTC
1 TT-TTTT-TTTTTTTC
2842200 TT
1 TT
2842202 CAAGCATAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
14 15 0.22
15 33 0.49
16 15 0.22
17 4 0.06
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTTTTTTTTTC
Found at i:2842175 original size:39 final size:39
Alignment explanation
Indices: 2842110--2842198 Score: 130
Period size: 39 Copynumber: 2.3 Consensus size: 39
2842100 TGACCCCTCA
*
2842110 TTTTT-TTTTCTTTCTTTTTTTCTTTTTTCTCTTTTTTC
1 TTTTTCTTTTTTTTCTTTTTTTCTTTTTTCTCTTTTTTC
*
2842148 TTTTTCTTTTTTTTCTTTTTCTT-TTTTTTTTCTTTTTTC
1 TTTTTCTTTTTTTTCTTTTT-TTCTTTTTTCTCTTTTTTC
2842187 -TTTTCTTTTTTT
1 TTTTTCTTTTTTT
2842199 CTTCAAGCAT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
38 17 0.36
39 28 0.60
40 2 0.04
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (39 bp):
TTTTTCTTTTTTTTCTTTTTTTCTTTTTTCTCTTTTTTC
Found at i:2854483 original size:15 final size:14
Alignment explanation
Indices: 2854459--2854500 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
2854449 CCTCGGTAAG
*
2854459 TTTCTCTTCTTTCTT
1 TTTCTTTTCTTTC-T
2854474 TTTCTTTTCTTTCT
1 TTTCTTTTCTTTCT
2854488 TTTCTGTTTCTTT
1 TTTCT-TTTCTTT
2854501 ACTGCGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 6 0.24
15 19 0.76
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.76
Consensus pattern (14 bp):
TTTCTTTTCTTTCT
Found at i:2854491 original size:20 final size:20
Alignment explanation
Indices: 2854459--2854500 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2854449 CCTCGGTAAG
*
2854459 TTTCTCTTCTTTCTTTTTCT
1 TTTCTCTTCTTTCTGTTTCT
2854479 TTTCT-TTCTTTTCTGTTTCT
1 TTTCTCTTC-TTTCTGTTTCT
2854499 TT
1 TT
2854501 ACTGCGTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTCTCTTCTTTCTGTTTCT
Found at i:2854587 original size:20 final size:20
Alignment explanation
Indices: 2854564--2854617 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
2854554 TCTCTCTCGG
2854564 TCTCTGTTGTTCTCCCTCTC
1 TCTCTGTTGTTCTCCCTCTC
*
2854584 TCTCTGTTGTTCTCCGTCTC
1 TCTCTGTTGTTCTCCCTCTC
2854604 TCTCTGTTGTTCTC
1 TCTCTGTTGTTCTC
2854618 TTTCCTTGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.00, C:0.35, G:0.13, T:0.52
Consensus pattern (20 bp):
TCTCTGTTGTTCTCCCTCTC
Found at i:2855036 original size:3 final size:3
Alignment explanation
Indices: 2855003--2855079 Score: 91
Period size: 3 Copynumber: 24.7 Consensus size: 3
2854993 CCGGGTTTTG
* * *
2855003 TAA TAT TAA TAAA TAAA TAA TATA TAT TAA TAA TAA TAA TAA TTA TAA
1 TAA TAA TAA T-AA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
*
2855051 TTA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2855080 TAAATAAAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
3 54 0.84
4 10 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:2866219 original size:26 final size:26
Alignment explanation
Indices: 2866190--2866242 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
2866180 TTTTTATCCT
2866190 TGTGGTCGTGGGATAGAGTCCCACGG
1 TGTGGTCGTGGGATAGAGTCCCACGG
*
2866216 TGTGGTCGTGGGATCGAGTCCCACGG
1 TGTGGTCGTGGGATAGAGTCCCACGG
2866242 T
1 T
2866243 AGGCAATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.13, C:0.21, G:0.42, T:0.25
Consensus pattern (26 bp):
TGTGGTCGTGGGATAGAGTCCCACGG
Found at i:2866477 original size:36 final size:33
Alignment explanation
Indices: 2866436--2866508 Score: 92
Period size: 33 Copynumber: 2.1 Consensus size: 33
2866426 ATTTTGAAGG
* *
2866436 TGTTCATGTTTGCATTCATTTAAATTTTCATAATCA
1 TGTTCATGTTTG--TTCATTT-AATGTTCATAAACA
*
2866472 TGTTCATGTTTGTTCATTTAGTGTTCATAAACA
1 TGTTCATGTTTGTTCATTTAATGTTCATAAACA
2866505 TGTT
1 TGTT
2866509 TATTTAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 15 0.44
34 7 0.21
36 12 0.35
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.51
Consensus pattern (33 bp):
TGTTCATGTTTGTTCATTTAATGTTCATAAACA
Found at i:2870040 original size:21 final size:21
Alignment explanation
Indices: 2870016--2870055 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2870006 ACTATCGCAT
2870016 TGCGATTTTCAAAATTCGCGC
1 TGCGATTTTCAAAATTCGCGC
**
2870037 TGCGATTTTCCGAATTCGC
1 TGCGATTTTCAAAATTCGC
2870056 AATGCGAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (21 bp):
TGCGATTTTCAAAATTCGCGC
Found at i:2870061 original size:21 final size:21
Alignment explanation
Indices: 2870010--2870062 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
2870000 ATTCTGACTA
*
2870010 TCGCATTGCGATTTTCAAAAT
1 TCGCAATGCGATTTTCAAAAT
** **
2870031 TCGCGCTGCGATTTTCCGAAT
1 TCGCAATGCGATTTTCAAAAT
2870052 TCGCAATGCGA
1 TCGCAATGCGA
2870063 ATATGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.32
Consensus pattern (21 bp):
TCGCAATGCGATTTTCAAAAT
Found at i:2870077 original size:20 final size:20
Alignment explanation
Indices: 2870052--2870107 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
2870042 TTTTCCGAAT
2870052 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATATGTAAA
2870072 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATATGTAAA
*
2870092 TCGCAATGCGATTATG
1 TCGCAATGCGAATATG
2870108 ACTATCGCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (20 bp):
TCGCAATGCGAATATGTAAA
Found at i:2870114 original size:20 final size:20
Alignment explanation
Indices: 2870091--2870198 Score: 162
Period size: 20 Copynumber: 5.4 Consensus size: 20
2870081 GAATATGTAA
* *
2870091 ATCGCAATGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
2870111 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
2870131 ATCGCAACGCGATTCTGATT
1 ATCGCAACGCGATTCTGACT
**
2870151 ATCGCAACAAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
2870171 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
2870191 GTCGCAAC
1 ATCGCAAC
2870199 ACTGAATTTC
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 79 1.00
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:2870115 original size:40 final size:39
Alignment explanation
Indices: 2870052--2870158 Score: 99
Period size: 40 Copynumber: 2.7 Consensus size: 39
2870042 TTTTCCGAAT
* * *
2870052 TCGCAATGCGAATATGTAAATCGCAATGCGAATATGTA-AA
1 TCGCAATGCGATTATG-ATATCGCAACGCGAATATG-ACAA
* * *
2870092 TCGCAATGCGATTATGACTATCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTATGA-TATCGCAACGCGAATATGACAA
* *
2870132 TCGCAACGCGATTCTGATTATCGCAAC
1 TCGCAATGCGATTATGA-TATCGCAAC
2870159 AAGATTCTGA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
39 2 0.04
40 54 0.96
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (39 bp):
TCGCAATGCGATTATGATATCGCAACGCGAATATGACAA
Found at i:2870135 original size:60 final size:60
Alignment explanation
Indices: 2870071--2870198 Score: 159
Period size: 60 Copynumber: 2.1 Consensus size: 60
2870061 GAATATGTAA
* ***
2870071 ATCGCAATGCGAATATG-TAAATCGCAATGCGATTATGACTATCGCAACGCGATTCTGACT
1 ATCGCAACGCGAATATGAT-AATCGCAACAAGATTATGACTATCGCAACGCGATTCTGACT
* * * *
2870131 ATCGCAACGCGATTCTGATTATCGCAACAAGATTCTGACTATCGCAACGCGATTCTGACT
1 ATCGCAACGCGAATATGATAATCGCAACAAGATTATGACTATCGCAACGCGATTCTGACT
*
2870191 GTCGCAAC
1 ATCGCAAC
2870199 ACTGAATTTC
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
60 57 0.98
61 1 0.02
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.26
Consensus pattern (60 bp):
ATCGCAACGCGAATATGATAATCGCAACAAGATTATGACTATCGCAACGCGATTCTGACT
Found at i:2871046 original size:24 final size:24
Alignment explanation
Indices: 2871019--2871072 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2871009 GTATTCGAAA
*
2871019 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGACAATACCCGGAC
* *
2871043 TTTGATCTTGGACAATACTCGGAT
1 TTTGATCTTGGACAATACCCGGAC
2871067 TTTGAT
1 TTTGAT
2871073 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATCTTGGACAATACCCGGAC
Found at i:2873194 original size:18 final size:18
Alignment explanation
Indices: 2873171--2873205 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2873161 AGAAAAAGGC
*
2873171 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
2873189 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
2873206 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:2873401 original size:20 final size:20
Alignment explanation
Indices: 2873376--2873664 Score: 238
Period size: 20 Copynumber: 15.4 Consensus size: 20
2873366 TTACACAATC
*
2873376 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
2873396 ATTTGACTATCGCAAAGCGA
1 ATTTGACTATCGCAACGCGA
* *
2873416 ATTTGATTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
* *
2873435 A----A-AATTGCAACGCGA
1 ATTTGACTATCGCAACGCGA
2873450 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
2873470 ATTTAACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
2873490 ATTTGACTATCGCAA--CGA
1 ATTTGACTATCGCAACGCGA
** *
2873508 A----AAAATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
*
2873524 ATTTGACTATTGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* **
2873544 ATTTGACTATCGCAGCTAGA
1 ATTTGACTATCGCAACGCGA
*
2873564 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* * *
2873584 ATTTGATTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGA
* *
2873604 ATTCGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* *
2873624 A----A--ATCGCAAAGCGT
1 ATTTGACTATCGCAACGCGA
*
2873638 ATTAGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
2873658 A-TTGACT
1 ATTTGACT
2873665 TTTGCGTTGC
Statistics
Matches: 213, Mismatches: 38, Indels: 37
0.74 0.13 0.13
Matches are distributed among these distances:
14 26 0.12
15 3 0.01
16 5 0.02
18 5 0.02
19 8 0.04
20 166 0.78
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:2873455 original size:34 final size:34
Alignment explanation
Indices: 2873404--2873541 Score: 159
Period size: 34 Copynumber: 3.9 Consensus size: 34
2873394 GAATTTGACT
* * *
2873404 ATCGCAAAGCGAATTTGATTATCGCAACTCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCAAAA
*
2873438 ATTGCAACGCGAATTTGACTATCGCAACGCGAATTTAA
1 ATCGCAACGCGAATTTGACTATCGCAACGC-AA---AA
*
2873476 CTATCGCAACGCGAATTTGACTATCGCAACGAAAAA
1 --ATCGCAACGCGAATTTGACTATCGCAACGCAAAA
* *
2873512 ATCGCAACACGAATTTGACTATTGCAACGC
1 ATCGCAACGCGAATTTGACTATCGCAACGC
2873542 GAATTTGACT
Statistics
Matches: 89, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
34 53 0.60
35 2 0.02
36 2 0.02
38 2 0.02
39 2 0.02
40 28 0.31
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (34 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCAAAA
Found at i:2873466 original size:74 final size:74
Alignment explanation
Indices: 2873376--2873580 Score: 297
Period size: 74 Copynumber: 2.8 Consensus size: 74
2873366 TTACACAATC
* * ** *
2873376 ATTTGAATATCGCAACGCGAATTTGACTATCGCAAAGCGAATTTGATTATCGCAACTCAAAAATT
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAAAGCGAATTTGACTATCGCAACGAAAAAATC
*
2873441 GCAACGCGA
66 GCAACACGA
* *
2873450 ATTTGACTATCGCAACGCGAATTTAACTATCGCAACGCGAATTTGACTATCGCAACGAAAAAATC
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAAAGCGAATTTGACTATCGCAACGAAAAAATC
2873515 GCAACACGA
66 GCAACACGA
*
2873524 ATTTGACTATTGCAACGCGAATTTGACTATCGC--AGCTAGAATTTGACTATCGCAACG
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAAAGC--GAATTTGACTATCGCAACG
2873581 TGAATTTGAT
Statistics
Matches: 118, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
72 2 0.02
74 116 0.98
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (74 bp):
ATTTGACTATCGCAACGCGAATTTGACTATCGCAAAGCGAATTTGACTATCGCAACGAAAAAATC
GCAACACGA
Found at i:2873576 original size:114 final size:113
Alignment explanation
Indices: 2873448--2873664 Score: 319
Period size: 114 Copynumber: 1.9 Consensus size: 113
2873438 ATTGCAACGC
*
2873448 GAATTTGACTATCGCAACGCGAATTTAACTATCGCAACGCGAATTTGACTATCGCAACGAAAAAA
1 GAATTTGACTATCGCAACGCGAATTTAACTATCGCAACGCGAATTCGACTATCGCAACGAAAAAA
* *
2873513 TCGCAACA-CGAATTTGACTATTGCAACGCGAATTTGACTATCGCAGCTA
66 TCGCAA-AGCGAATTAGACTATCGCAACGCGAA-TTGACTATCGCAGCTA
* * * * * *
2873562 GAATTTGACTATCGCAACGTGAATTTGATTATCGCAACGGGTATTCGACTATCGCAACGAGAAAA
1 GAATTTGACTATCGCAACGCGAATTTAACTATCGCAACGCGAATTCGACTATCGCAACGAAAAAA
*
2873627 TCGCAAAGCGTATTAGACTATCGCAACGCGAATTGACT
66 TCGCAAAGCGAATTAGACTATCGCAACGCGAATTGACT
2873665 TTTGCGTTGC
Statistics
Matches: 92, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
113 7 0.08
114 85 0.92
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (113 bp):
GAATTTGACTATCGCAACGCGAATTTAACTATCGCAACGCGAATTCGACTATCGCAACGAAAAAA
TCGCAAAGCGAATTAGACTATCGCAACGCGAATTGACTATCGCAGCTA
Found at i:2873660 original size:94 final size:94
Alignment explanation
Indices: 2873376--2873664 Score: 282
Period size: 94 Copynumber: 3.1 Consensus size: 94
2873366 TTACACAATC
* * * * *
2873376 ATTTGAATATCGCAACGCGAATTTGACTATCGCAAAGCGAATTTGATTATCGCAACTCA-AAAAT
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAGAATTCGACTATCGCAAC-CAGAAAAT
2873440 TGCAACGCGAATTTGACTATCGCAACGCGA
65 TGCAACGCGAATTTGACTATCGCAACGCGA
* * * *** **
2873470 ATTTAACTATCGCAACGCGAATTTGACTATCGCAACGAAAAAATCGCAAC-A-CG-AATTTGACT
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACG-AGAATTCG--ACTATCGCAACCAGAAA
* **
2873532 ATTGCAACGCGAATTTGACTATCGCAGCTAGA
63 ATTGCAACGCGAATTTGACTATCGCAACGCGA
* * * * * *
2873564 ATTTGACTATCGCAACGTGAATTTGATTATCGCAACGGGTATTCGACTATCGCAACGAGAAAATC
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAGAATTCGACTATCGCAACCAGAAAATT
* * *
2873629 GCAAAGCGTATTAGACTATCGCAACGCGA
66 GCAACGCGAATTTGACTATCGCAACGCGA
2873658 A-TTGACT
1 ATTTGACT
2873665 TTTGCGTTGC
Statistics
Matches: 153, Mismatches: 35, Indels: 15
0.75 0.17 0.07
Matches are distributed among these distances:
91 2 0.01
92 1 0.01
93 12 0.08
94 130 0.85
95 6 0.04
96 1 0.01
97 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (94 bp):
ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAGAATTCGACTATCGCAACCAGAAAATT
GCAACGCGAATTTGACTATCGCAACGCGA
Found at i:2873714 original size:20 final size:20
Alignment explanation
Indices: 2873663--2873716 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
2873653 CGCGAATTGA
*
2873663 CTTTTGCGTTGCGATTTTGG
1 CTTTAGCGTTGCGATTTTGG
* *
2873683 CTTTCGCATTGCGATTTTGAG
1 CTTTAGCGTTGCGATTTTG-G
2873704 -TTTAGCGTTGCGA
1 CTTTAGCGTTGCGA
2873717 AAATGTACCT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.11, C:0.17, G:0.28, T:0.44
Consensus pattern (20 bp):
CTTTAGCGTTGCGATTTTGG
Found at i:2873857 original size:14 final size:14
Alignment explanation
Indices: 2873838--2873874 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
2873828 TCAATATTAA
2873838 ACAAATCAACTTTT
1 ACAAATCAACTTTT
2873852 ACAAATCAACTTTT
1 ACAAATCAACTTTT
2873866 ACAAATCAA
1 ACAAATCAA
2873875 TTAAACAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2875339 original size:21 final size:21
Alignment explanation
Indices: 2875306--2875355 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
2875296 TGACAGTGGC
*
2875306 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGAGAGGGGA
** * *
2875327 CTCTTGAGGGGTGATAGGGGC
1 CTCTTGAACGGTGAGAGGGGA
2875348 CTCTTGAA
1 CTCTTGAA
2875356 TGATAGGGGA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.16, G:0.42, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGAGAGGGGA
Found at i:2875477 original size:18 final size:18
Alignment explanation
Indices: 2875456--2875495 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
2875446 CACGTGCACG
2875456 CCGTTTGATGCGTGAACT
1 CCGTTTGATGCGTGAACT
2875474 CCGTTTGATGCGTGAACT
1 CCGTTTGATGCGTGAACT
2875492 CCGT
1 CCGT
2875496 CTTGTAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.15, C:0.25, G:0.28, T:0.33
Consensus pattern (18 bp):
CCGTTTGATGCGTGAACT
Found at i:2875926 original size:20 final size:20
Alignment explanation
Indices: 2875901--2875956 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
2875891 TCGCAACACG
*
2875901 AATGACTATCGCAACGTGAA
1 AATGACTATCGCAACGCGAA
2875921 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
**
2875941 TTTGACTATCGCAACG
1 AATGACTATCGCAACG
2875957 AGAGAATCGC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:2876025 original size:20 final size:20
Alignment explanation
Indices: 2876000--2876087 Score: 95
Period size: 20 Copynumber: 4.4 Consensus size: 20
2875990 GCGATTCTTT
*
2876000 CGTTGCGATAGTTAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
2876020 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* ** *
2876040 CGTTACGATAGTCATTTTCA
1 CGTTGCGATAGTCAAATTCG
* **
2876060 CGTTGTGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
2876080 CGTTGCGA
1 CGTTGCGA
2876088 AAGTAAACTA
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:2876395 original size:21 final size:21
Alignment explanation
Indices: 2876368--2876420 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
2876358 TGCACCATTG
*
2876368 TCATCACGTAAAGTATCGACC
1 TCATCACGTAAAGCATCGACC
* * * *
2876389 TCCTCACGCAAGGCATTGACC
1 TCATCACGTAAAGCATCGACC
2876410 TCATCACGTAA
1 TCATCACGTAA
2876421 CTCCCCTAAC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.30, C:0.32, G:0.15, T:0.23
Consensus pattern (21 bp):
TCATCACGTAAAGCATCGACC
Found at i:2877961 original size:20 final size:20
Alignment explanation
Indices: 2877938--2878024 Score: 97
Period size: 20 Copynumber: 4.5 Consensus size: 20
2877928 TCTGAAACTT
*
2877938 AAAATCGCAACACGAAAATA
1 AAAATCGCAACACGAAAATG
*
2877958 AAAATTGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
2877978 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
* *
2877997 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACACGAAAATG
2878016 AAAATCGCA
1 AAAATCGCA
2878025 TTGCGATTCT
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
19 26 0.46
20 31 0.54
ACGTcount: A:0.51, C:0.22, G:0.15, T:0.13
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:2877997 original size:19 final size:19
Alignment explanation
Indices: 2877938--2878024 Score: 86
Period size: 19 Copynumber: 4.5 Consensus size: 19
2877928 TCTGAAACTT
* *
2877938 AAAATCGCAACACGAAAATA
1 AAAATCGCAACGCG-AAATG
* *
2877958 AAAATTGCAACACGAAAATG
1 AAAATCGCAACGCG-AAATG
**
2877978 ACTATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
2877997 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACGCGAAA-TG
2878016 AAAATCGCA
1 AAAATCGCA
2878025 TTGCGATTCT
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
19 29 0.50
20 29 0.50
ACGTcount: A:0.51, C:0.22, G:0.15, T:0.13
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:2878418 original size:22 final size:22
Alignment explanation
Indices: 2878391--2878433 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2878381 GAGATAGAAG
*
2878391 GATTTCACCGGAGATGGGGACT
1 GATTTCACCAGAGATGGGGACT
**
2878413 GATTTCGTCAGAGATGGGGAC
1 GATTTCACCAGAGATGGGGAC
2878434 GGATGTCGCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.16, G:0.37, T:0.23
Consensus pattern (22 bp):
GATTTCACCAGAGATGGGGACT
Found at i:2878642 original size:20 final size:20
Alignment explanation
Indices: 2878609--2878702 Score: 134
Period size: 20 Copynumber: 4.7 Consensus size: 20
2878599 GCGCTTTGAA
* *
2878609 AATCGCATTACGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
2878629 CATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
2878649 AATCTCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
2878669 AATCGCGTTGCGATAGTCAT
1 AATCGCGTTGCGATAGTCAG
*
2878689 AATCGCATTGCGAT
1 AATCGCGTTGCGAT
2878703 TTACATATTC
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 66 1.00
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:2878709 original size:20 final size:20
Alignment explanation
Indices: 2878686--2878741 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
2878676 TTGCGATAGT
*
2878686 CATAATCGCATTGCGATTTA
1 CATATTCGCATTGCGATTTA
2878706 CATATTCGCATTGCGATTTA
1 CATATTCGCATTGCGATTTA
2878726 CATATTCGCATTGCGA
1 CATATTCGCATTGCGA
2878742 ATTCAGAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (20 bp):
CATATTCGCATTGCGATTTA
Found at i:2878762 original size:21 final size:21
Alignment explanation
Indices: 2878738--2878778 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2878728 TATTCGCATT
2878738 GCGAATTCAGAAAATCGCAAC
1 GCGAATTCAGAAAATCGCAAC
**
2878759 GCGAATTTGGAAAATCGCAA
1 GCGAATTCAGAAAATCGCAA
2878779 TGCAATAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.17
Consensus pattern (21 bp):
GCGAATTCAGAAAATCGCAAC
Found at i:2879647 original size:2 final size:2
Alignment explanation
Indices: 2879640--2879667 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2879630 CTCGTTGAGG
2879640 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2879668 ATTTTTCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2882630 original size:3 final size:3
Alignment explanation
Indices: 2882622--2882663 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
2882612 CCTACAAGAA
*
2882622 AAT AAT AAT AAT AA- AAT AAT AAT AAT AAA AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2882664 AGACGGGTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 4 0.11
3 31 0.89
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:2882639 original size:14 final size:14
Alignment explanation
Indices: 2882620--2882664 Score: 74
Period size: 14 Copynumber: 3.2 Consensus size: 14
2882610 AGCCTACAAG
2882620 AAAATAATAATAAT
1 AAAATAATAATAAT
2882634 AAAATAATAATAAT
1 AAAATAATAATAAT
2882648 AAAAATAATAA-AAT
1 -AAAATAATAATAAT
2882662 AAA
1 AAA
2882665 GACGGGTTCG
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
13 3 0.10
14 17 0.57
15 10 0.33
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AAAATAATAATAAT
Found at i:2883362 original size:38 final size:38
Alignment explanation
Indices: 2883290--2883537 Score: 169
Period size: 38 Copynumber: 6.2 Consensus size: 38
2883280 CTTAATAAGG
*
2883290 GAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGA
1 GAGTCAAGAATAAC----AAAGATTGACTTCTCTTCACGAGA
* *
2883332 GAGTCAAGAATAACAAAGACTAACTTCTCTTCACGAGA
1 GAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGA
* * * *
2883370 AAGTTAAGAATAACATTGAAATATTGACTCCTCTTCACGATG-
1 GAGTCAAGAATAAC----AAAGATTGACTTCTCTTCACGA-GA
* * * *
2883412 GAGTTAGGAATAAAAAAAGATTGACTTCTCTTCATGA-A
1 GAGTCAAGAAT-AACAAAGATTGACTTCTCTTCACGAGA
* * *
2883450 GAAGTCAAAAATAACAAAGATCGACTTCTCTTCAAGAG-
1 G-AGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGA
* * * *
2883488 GAAGTCAATAATAACATTGAAAGATTGACTCCACTTCGCGAGA
1 G-AGTCAAGAATAAC----AAAGATTGACTTCTCTTCACGAGA
2883531 GAGTCAA
1 GAGTCAA
2883538 ATTGAAGCTT
Statistics
Matches: 165, Mismatches: 27, Indels: 28
0.75 0.12 0.13
Matches are distributed among these distances:
38 70 0.42
39 26 0.16
42 65 0.39
43 4 0.02
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.25
Consensus pattern (38 bp):
GAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGA
Found at i:2883396 original size:80 final size:81
Alignment explanation
Indices: 2883295--2883445 Score: 225
Period size: 80 Copynumber: 1.9 Consensus size: 81
2883285 TAAGGGAGTC
*
2883295 AAGAATAACATTGAAAGATTGACTCCTCTTCACGA-GAGAGTCAAGAAT-AACAAAGACTAACTT
1 AAGAATAACATTGAAAGATTGACTCCTCTTCACGATG-GAGTCAAGAATAAAAAAAGACTAACTT
2883358 CTCTTCACGAGAAAGTT
65 CTCTTCACGAGAAAGTT
* * * * *
2883375 AAGAATAACATTGAAATATTGACTCCTCTTCACGATGGAGTTAGGAATAAAAAAAGATTGACTTC
1 AAGAATAACATTGAAAGATTGACTCCTCTTCACGATGGAGTCAAGAATAAAAAAAGACTAACTTC
2883440 TCTTCA
66 TCTTCA
2883446 TGAAGAAGTC
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
80 43 0.68
81 20 0.32
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.26
Consensus pattern (81 bp):
AAGAATAACATTGAAAGATTGACTCCTCTTCACGATGGAGTCAAGAATAAAAAAAGACTAACTTC
TCTTCACGAGAAAGTT
Found at i:2883457 original size:119 final size:119
Alignment explanation
Indices: 2883308--2883524 Score: 312
Period size: 119 Copynumber: 1.8 Consensus size: 119
2883298 AATAACATTG
* *
2883308 AAAGATTGACTCCTCTTCACGAGAGAGTCAAGAATAACAAAGA-CTAACTTCTCTTCACGAGAAA
1 AAAGATTGACTCCTCTTCACGAGAGAGTCAAAAATAACAAAGATC-AACTTCTCTTCAAGAGAAA
* * *
2883372 GTTAAGAATAACATTGAAATATTGACTCCTCTTCACGATGGAGTTAGGAATAAAA
65 GTCAAGAATAACATTGAAAGATTGACTCCACTTCACGATGGAGTTAGGAATAAAA
* * * *
2883427 AAAGATTGACTTCTCTTCATGA-AGAAGTCAAAAATAACAAAGATCGACTTCTCTTCAAGAGGAA
1 AAAGATTGACTCCTCTTCACGAGAG-AGTCAAAAATAACAAAGATCAACTTCTCTTCAAGAGAAA
*
2883491 GTCAATAATAACATTGAAAGATTGACTCCACTTC
65 GTCAAGAATAACATTGAAAGATTGACTCCACTTC
2883525 GCGAGAGAGT
Statistics
Matches: 86, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
118 2 0.02
119 83 0.97
120 1 0.01
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.26
Consensus pattern (119 bp):
AAAGATTGACTCCTCTTCACGAGAGAGTCAAAAATAACAAAGATCAACTTCTCTTCAAGAGAAAG
TCAAGAATAACATTGAAAGATTGACTCCACTTCACGATGGAGTTAGGAATAAAA
Found at i:2884447 original size:216 final size:217
Alignment explanation
Indices: 2884176--2884593 Score: 651
Period size: 217 Copynumber: 1.9 Consensus size: 217
2884166 GAACTTACCT
* *
2884176 ATTTTGGAAATAGTTTATAAGATAAGAAACTTTGGAAATCTCTTTTTTACTTTTCAAAATTTTCA
1 ATTTTGGAAATAGTTTATAAGATAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAATTTTCA
2884241 -TTTTTGAAAATACTAAATGAGAAAATTTGGAAATCAATTTCTCATTTTTCAAATTCATATGAAA
66 TTTTTTGAAAATACTAAATGAGAAAATTTGGAAATCAATTTCTCATTTTTCAAATTCATATGAAA
* *
2884305 ACATCCTACCCAAAGGTCTTACGGATGGCCCAAAGGACTTATCATCTCACTCGAAAGACTAACAG
131 ACATCCTACCCAAAGGTCTTACGAATGGCCCAAAGGACTTATCATCTCACTAGAAAGACTAACAG
2884370 ATGACCCACTGAGGACTTATTA
196 ATGACCCACTGAGGACTTATTA
* *
2884392 ATTTTGGAAATAGTTTACT-GGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAATTTTC
1 ATTTTGGAAATAGTTTA-TAAGATAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAATTTTC
* * * * *
2884456 ATTTTTTGAAAATACTAAATGGGAAACTTTGGATATCACTTTCTCATTTTTCAAATTCATGTGAA
65 ATTTTTTGAAAATACTAAATGAGAAAATTTGGAAATCAATTTCTCATTTTTCAAATTCATATGAA
* ** * ** *
2884521 AACATCCTACCCAAAGGTCTTATGAATGGCCTGAAGGATTTATCATCTTGCTAGAAAGACTTACA
130 AACATCCTACCCAAAGGTCTTACGAATGGCCCAAAGGACTTATCATCTCACTAGAAAGACTAACA
2884586 GATGACCC
195 GATGACCC
2884594 GAAGGATTTA
Statistics
Matches: 182, Mismatches: 18, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
216 59 0.32
217 123 0.68
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (217 bp):
ATTTTGGAAATAGTTTATAAGATAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAATTTTCA
TTTTTTGAAAATACTAAATGAGAAAATTTGGAAATCAATTTCTCATTTTTCAAATTCATATGAAA
ACATCCTACCCAAAGGTCTTACGAATGGCCCAAAGGACTTATCATCTCACTAGAAAGACTAACAG
ATGACCCACTGAGGACTTATTA
Found at i:2884625 original size:42 final size:42
Alignment explanation
Indices: 2884553--2884646 Score: 118
Period size: 42 Copynumber: 2.3 Consensus size: 42
2884543 TGAATGGCCT
* *
2884553 GAAGGATTT-ATCATCTTGCTAGAAAGACTTACAGATGACCC
1 GAAGGATTTAAGCATCATGCTAGAAAGACTTACAGATGACCC
* * * *
2884594 GAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCT
1 GAAGGATTTAAGCATCATGCTAGAAAGACTTACAGATGACCC
*
2884636 GAAGGACTTAA
1 GAAGGATTTAA
2884647 AAATTTTGGA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 9 0.20
42 36 0.80
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (42 bp):
GAAGGATTTAAGCATCATGCTAGAAAGACTTACAGATGACCC
Found at i:2884837 original size:257 final size:256
Alignment explanation
Indices: 2884322--2885147 Score: 1043
Period size: 257 Copynumber: 3.2 Consensus size: 256
2884312 ACCCAAAGGT
* * * * * * **
2884322 CTTACGGATGGCCCAAAGGACTT-ATCATC-TCACTCGAAAGACTAACAGATGACCCACTGAGGA
1 CTTACAGATGACCCAAAGGATTTAATCATCAT-GCTCGAAAGACTTACTGATGGTCCA--GAGGA
**
2884385 CTTATTAATTTTGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAA
63 CTTAAAAATTTTGGAAATAGTTTACT-GGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAA
* * * * * * *
2884450 ATTTTCATTTTTTGAAAATACTAAATGGGAAACTTTGGATATCACTTTCTCATTTTTCAAATTCA
127 ATTTTCATTTTCTAAAAACATTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAATTCA
* * ** *
2884515 TGTGAAAACATCCTACCCAAAGGTCTTATGAATGGCCTGAAGGATTTATCATCTTGCTAGAAAGA
192 TGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCAAAGGACTTATCATCTTGCTAGAAAGA
* * *
2884580 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGG-CCTGAAGGACT
1 CTTACAGATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGTCCAG-AGGACT
* *
2884644 TAAAAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAA
65 TAAAAATTTTGGAAATAGTTTACT-GGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAT
* * * * *
2884709 TTTCATTTTCTAAAAACATTAAATAAGAATCTTTGGAAACCGCTTTCTCATTTTTCAATTTAATG
129 TTTCATTTTCTAAAAACATTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAATTCATG
* *
2884774 TGAAAACATCCTACCCGAAGGTCTTACGGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGA
194 TGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCAAAGGACTTATCATCTTGCTAGAAAGA
* * *
2884837 CTTATAGATGA-CCTAAGGAATTTAATCATCATGCTCGAAAGACTTACTGATGGTCCAGACGACT
1 CTTACAGATGACCCAAAGG-ATTTAATCATCATGCTCGAAAGACTTACTGATGGTCCAGAGGACT
* * *
2884901 TACAAATTTTGGAAATAGTTTACTGGCTAAGAAACTTTGGAAATCGTTTTCTTAGTTTTCAAAAT
65 TAAAAATTTTGGAAATAGTTTACTGG-TAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAT
* * * * *
2884966 TTTCATTATC-AGAAAAGATTTAAATGAGAAAAATTTGGAAATCGTTTTCTTATTTTTCAAATTC
129 TTTCATTTTCTA-AAAACA-TTAAATGAG-AAACTTTGGAAATCGCTTTCTCATTTTTCAAATTC
* *
2885030 ATGTGAAAACATCCTACCAGAAGGTCTTATGGATGG-CCAGAAGGACTTATCATCTTGCTTGAAA
191 ATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCA-AAGGACTTATCATCTTGCTAGAAA
2885094 GA
255 GA
* * **
2885096 CTAACAGATGACCAAAAGGATTTAATCATCATGCTTAAAAGACTTACTGATG
1 CTTACAGATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATG
2885148 ACCCGAAAGA
Statistics
Matches: 494, Mismatches: 63, Indels: 21
0.85 0.11 0.04
Matches are distributed among these distances:
256 10 0.02
257 294 0.60
258 35 0.07
259 149 0.30
260 6 0.01
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (256 bp):
CTTACAGATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGTCCAGAGGACTT
AAAAATTTTGGAAATAGTTTACTGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAATTT
TCATTTTCTAAAAACATTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAATTCATGTG
AAAACATCCTACCCGAAGGTCTTATGGATGGCCCAAAGGACTTATCATCTTGCTAGAAAGA
Found at i:2885131 original size:42 final size:41
Alignment explanation
Indices: 2885061--2885150 Score: 108
Period size: 42 Copynumber: 2.2 Consensus size: 41
2885051 AGGTCTTATG
* * * *
2885061 GATGGCCAGAAGGACTTATCATCTTGCTTGAAAGACTAACA
1 GATGACCAAAAGGACTTATCATCATGCTTAAAAGACTAACA
* * *
2885102 GATGACCAAAAGGATTTAATCATCATGCTTAAAAGACTTACT
1 GATGACCAAAAGGACTT-ATCATCATGCTTAAAAGACTAACA
2885144 GATGACC
1 GATGACC
2885151 CGAAAGAATT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 14 0.34
42 27 0.66
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26
Consensus pattern (41 bp):
GATGACCAAAAGGACTTATCATCATGCTTAAAAGACTAACA
Found at i:2886937 original size:8 final size:8
Alignment explanation
Indices: 2886916--2887009 Score: 71
Period size: 8 Copynumber: 11.2 Consensus size: 8
2886906 ATTTGATTTA
2886916 CTTTTTCTT
1 CTTTTT-TT
*
2886925 ATTTTTTT
1 CTTTTTTT
*
2886933 CTTTTTCT
1 CTTTTTTT
*
2886941 CTCTTTTT
1 CTTTTTTT
2886949 CTTTTTCTT
1 CTTTTT-TT
2886958 CTTTTTTT
1 CTTTTTTT
*
2886966 ATTTTTTT
1 CTTTTTTT
* *
2886974 ATCTTTTCT
1 CT-TTTTTT
*
2886983 CTATTTTT
1 CTTTTTTT
*
2886991 CTTATTTTC
1 CTT-TTTTT
*
2887000 CTATTTTT
1 CTTTTTTT
2887008 CT
1 CT
2887010 ATCTTTTTAT
Statistics
Matches: 67, Mismatches: 15, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
8 42 0.63
9 25 0.37
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (8 bp):
CTTTTTTT
Found at i:2886970 original size:16 final size:15
Alignment explanation
Indices: 2886917--2886970 Score: 54
Period size: 17 Copynumber: 3.3 Consensus size: 15
2886907 TTTGATTTAC
*
2886917 TTTTTCTTATTTTTTT
1 TTTTTCTT-CTTTTTT
*
2886933 CTTTTTCTCTCTTTTTC
1 -TTTTTCT-TCTTTTTT
2886950 TTTTTCTTCTTTTTT
1 TTTTTCTTCTTTTTT
2886965 TATTTT
1 T-TTTT
2886971 TTTATCTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
15 8 0.25
16 11 0.34
17 12 0.38
18 1 0.03
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTCTTCTTTTTT
Found at i:2886990 original size:36 final size:33
Alignment explanation
Indices: 2886916--2887017 Score: 123
Period size: 33 Copynumber: 3.0 Consensus size: 33
2886906 ATTTGATTTA
* *
2886916 CTTTTTCTTATTTTTTTCTTTTTCTCTCTTTTT
1 CTTTTTCTTATTTTTTTATTTTTCTATCTTTTT
* *
2886949 CTTTTTCTTCTTTTTTTATTTTTTTATCTTTTCT
1 CTTTTTCTTATTTTTTTATTTTTCTATCTTTT-T
**
2886983 CTATTTTTCTTATTTTCCTATTTTTCTATCTTTTT
1 C--TTTTTCTTATTTTTTTATTTTTCTATCTTTTT
2887018 ATGAATTTAT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
33 28 0.48
34 2 0.03
35 1 0.02
36 27 0.47
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (33 bp):
CTTTTTCTTATTTTTTTATTTTTCTATCTTTTT
Found at i:2887003 original size:17 final size:17
Alignment explanation
Indices: 2886950--2887009 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
2886940 TCTCTTTTTC
* **
2886950 TTTTTCTTCTTTTTTTA
1 TTTTTCTTATTTTCCTA
2886967 TTTTT-TTATCTTTTCTCTA
1 TTTTTCTTA--TTTTC-CTA
2886986 TTTTTCTTATTTTCCTA
1 TTTTTCTTATTTTCCTA
2887003 TTTTTCT
1 TTTTTCT
2887010 ATCTTTTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
16 2 0.06
17 15 0.42
18 9 0.25
19 7 0.19
20 3 0.08
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTTCTTATTTTCCTA
Found at i:2891302 original size:20 final size:20
Alignment explanation
Indices: 2891277--2891315 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2891267 GCACTCGAAT
2891277 TAAAATAATAATCACAAAGA
1 TAAAATAATAATCACAAAGA
*
2891297 TAAAATAATAATCATAAAG
1 TAAAATAATAATCACAAAG
2891316 GACTAAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.64, C:0.08, G:0.05, T:0.23
Consensus pattern (20 bp):
TAAAATAATAATCACAAAGA
Found at i:2892336 original size:2 final size:2
Alignment explanation
Indices: 2892331--2892357 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2892321 TGTTTGTGTG
2892331 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 T
2892358 CGAATAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2892863 original size:3 final size:3
Alignment explanation
Indices: 2892855--2892894 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
2892845 TACAAGAAAT
*
2892855 TAA TAA TAA TAA TTA -AA TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2892895 AGACGGATCC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 3 0.09
3 30 0.91
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2892880 original size:20 final size:20
Alignment explanation
Indices: 2892855--2892894 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2892845 TACAAGAAAT
*
2892855 TAATAATAATAATTAAATAA
1 TAATAATAATAATAAAATAA
2892875 TAATAATAATAATAAAATAA
1 TAATAATAATAATAAAATAA
2892895 AGACGGATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
TAATAATAATAATAAAATAA
Found at i:2894828 original size:15 final size:13
Alignment explanation
Indices: 2894812--2894838 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2894802 TATATATATA
2894812 TATATAGAAAATT
1 TATATAGAAAATT
2894825 TATATAGAAAATT
1 TATATAGAAAATT
2894838 T
1 T
2894839 TTTGGAAAAT
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:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (13 bp):
TATATAGAAAATT
Found at i:2895852 original size:18 final size:18
Alignment explanation
Indices: 2895798--2895852 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
2895788 TGTCCATATC
*
2895798 TTTTCCTATATTG-TTAT
1 TTTTCCTATATTGTTTCT
* * *
2895815 TTTCCCTGTACTT-TTCCT
1 TTTTCCTATA-TTGTTTCT
2895833 TTTTCCTATATTGTTTCT
1 TTTTCCTATATTGTTTCT
2895851 TT
1 TT
2895853 ACTATACTAT
Statistics
Matches: 28, Mismatches: 7, Indels: 5
0.70 0.17 0.12
Matches are distributed among these distances:
17 10 0.36
18 18 0.64
ACGTcount: A:0.11, C:0.20, G:0.05, T:0.64
Consensus pattern (18 bp):
TTTTCCTATATTGTTTCT
Found at i:2895872 original size:17 final size:17
Alignment explanation
Indices: 2895850--2895904 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
2895840 ATATTGTTTC
2895850 TTTACTATACTATATCT
1 TTTACTATACTATATCT
* *
2895867 TTTACTATATTGTTAT-T
1 TTTACTATACT-ATATCT
* *
2895884 TTTACTGTACTATTTCT
1 TTTACTATACTATATCT
2895901 TTTA
1 TTTA
2895905 ATTTCATTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
16 2 0.07
17 25 0.83
18 3 0.10
ACGTcount: A:0.24, C:0.13, G:0.04, T:0.60
Consensus pattern (17 bp):
TTTACTATACTATATCT
Found at i:2895888 original size:34 final size:34
Alignment explanation
Indices: 2895793--2895904 Score: 120
Period size: 34 Copynumber: 3.3 Consensus size: 34
2895783 TGTATTGTCC
* **
2895793 ATATCTTTTCCTATATTGTTATTTTCCCTGTACT
1 ATATCTTTTACTATATTGTTATTTTTACTGTACT
* * * *
2895827 -TTTCCTTTTTCCTATATTGTT-TCTTTACTATACT
1 ATAT-C-TTTTACTATATTGTTATTTTTACTGTACT
2895861 ATATCTTTTACTATATTGTTATTTTTACTGTACT
1 ATATCTTTTACTATATTGTTATTTTTACTGTACT
*
2895895 ATTTCTTTTA
1 ATATCTTTTA
2895905 ATTTCATTTT
Statistics
Matches: 64, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
33 16 0.25
34 31 0.48
35 17 0.27
ACGTcount: A:0.19, C:0.17, G:0.04, T:0.60
Consensus pattern (34 bp):
ATATCTTTTACTATATTGTTATTTTTACTGTACT
Found at i:2897235 original size:20 final size:21
Alignment explanation
Indices: 2897211--2897280 Score: 63
Period size: 20 Copynumber: 3.3 Consensus size: 21
2897201 ATATCTAAAG
2897211 TTAATTAAATATATGTTTTAA
1 TTAATTAAATATATGTTTTAA
* * *
2897232 -TAATCCTGAATATTTAGTTTCAA
1 TTAAT--TAAATATAT-GTTTTAA
*
2897255 TTAATTAAATATA-GATTTAA
1 TTAATTAAATATATGTTTTAA
2897275 TTAATT
1 TTAATT
2897281 TGAAATAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
20 15 0.39
22 13 0.34
23 6 0.16
24 4 0.11
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.49
Consensus pattern (21 bp):
TTAATTAAATATATGTTTTAA
Found at i:2900633 original size:30 final size:30
Alignment explanation
Indices: 2900597--2900687 Score: 121
Period size: 30 Copynumber: 3.0 Consensus size: 30
2900587 ATTAATATTA
* *
2900597 TGCATCGATACACTACAGTAGCTACTACAG
1 TGCATCGATACGCTACAGTAACTACTACAG
*
2900627 TGCATCGATACGCTACAGTAACGGA-TACAG
1 TGCATCGATACGCTACAGTAAC-TACTACAG
* *
2900657 TGCATCAATACGCTACAGTAACTGCTACAG
1 TGCATCGATACGCTACAGTAACTACTACAG
2900687 T
1 T
2900688 AACTTCCGAA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
30 52 0.98
31 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (30 bp):
TGCATCGATACGCTACAGTAACTACTACAG
Found at i:2901188 original size:44 final size:45
Alignment explanation
Indices: 2901068--2901193 Score: 182
Period size: 47 Copynumber: 2.8 Consensus size: 45
2901058 TATAAAATCT
*
2901068 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
2901113 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCAATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
2901160 CTTGCCA-TTATTCCATAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
2901194 GCATGGTTAC
Statistics
Matches: 74, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
44 24 0.32
45 10 0.14
46 2 0.03
47 38 0.51
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:2901353 original size:40 final size:40
Alignment explanation
Indices: 2901298--2901419 Score: 235
Period size: 40 Copynumber: 3.0 Consensus size: 40
2901288 ACTGTAGTGC
2901298 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2901338 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
2901378 TACACATAAGGTCATGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2901418 TA
1 TA
2901420 TAAACCTGCA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 81 1.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:2904165 original size:18 final size:17
Alignment explanation
Indices: 2904137--2904171 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
2904127 ATATTTATTT
2904137 ATATGAAATATAATATA
1 ATATGAAATATAATATA
2904154 ATATGAAAATATAATATA
1 ATATG-AAATATAATATA
2904172 TCATCTCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (17 bp):
ATATGAAATATAATATA
Found at i:2921644 original size:16 final size:16
Alignment explanation
Indices: 2921623--2921655 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2921613 CATACGTAGC
2921623 TAATTTTCTTTTAAGT
1 TAATTTTCTTTTAAGT
2921639 TAATTTTCTTTTAAGT
1 TAATTTTCTTTTAAGT
2921655 T
1 T
2921656 GAAGGCTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.64
Consensus pattern (16 bp):
TAATTTTCTTTTAAGT
Found at i:2921943 original size:18 final size:18
Alignment explanation
Indices: 2921920--2921962 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
2921910 CTTTATATTA
*
2921920 TTTATTTAATTATTTTAT
1 TTTATTTAATTATTATAT
* *
2921938 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATAT
2921956 TTTATTT
1 TTTATTT
2921963 TAAAAACAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATAT
Found at i:2922019 original size:8 final size:8
Alignment explanation
Indices: 2922001--2922046 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
2921991 TCTTTACTAC
2922001 TATTA-TT
1 TATTATTT
2922008 TATTATTT
1 TATTATTT
2922016 TATTATTT
1 TATTATTT
*
2922024 TA-TCTTT
1 TATTATTT
2922031 TATTGTATTT
1 TA-T-TATTT
2922041 TATTAT
1 TATTAT
2922047 AACATTTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
7 11 0.33
8 15 0.45
9 1 0.03
10 6 0.18
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (8 bp):
TATTATTT
Found at i:2922046 original size:20 final size:21
Alignment explanation
Indices: 2922001--2922046 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
2921991 TCTTTACTAC
*
2922001 TATTATTTATTATTTTATTAT
1 TATTATTTATTATTGTATTAT
2922022 T-TTATCTT-TTATTGTATT-T
1 TATTAT-TTATTATTGTATTAT
2922041 TATTAT
1 TATTAT
2922047 AACATTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 2 0.09
20 17 0.77
21 3 0.14
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (21 bp):
TATTATTTATTATTGTATTAT
Found at i:2922096 original size:42 final size:42
Alignment explanation
Indices: 2922010--2922096 Score: 104
Period size: 43 Copynumber: 2.1 Consensus size: 42
2922000 CTATTATTTA
* *
2922010 TTATTTTATTATTTTATCTTTTATTGTATTTTATTATAACAT
1 TTATTTTATTATTTTATCTTTCATTGTATTTTATTATAAAAT
* * * *
2922052 TTATTTTACTTTTTTTTTCTTTCCTTGTATTTTCTT-TAAAAT
1 TTATTTTA-TTATTTTATCTTTCATTGTATTTTATTATAAAAT
2922094 TTA
1 TTA
2922097 ACACTTTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 16 0.42
43 22 0.58
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.68
Consensus pattern (42 bp):
TTATTTTATTATTTTATCTTTCATTGTATTTTATTATAAAAT
Found at i:2922123 original size:34 final size:29
Alignment explanation
Indices: 2922076--2922146 Score: 70
Period size: 30 Copynumber: 2.2 Consensus size: 29
2922066 TTTTCTTTCC
2922076 TTGTATTTTCTTTAAAATTTAACACTTTTTTATT
1 TTGT-TTTTCTTT--AATTTAACAC--TTTTATT
* *
2922110 TTGTTTTATCTTTATTTTCACACTTTTATT
1 TTGTTTT-TCTTTAATTTAACACTTTTATT
2922140 TTGTTTT
1 TTGTTTT
2922147 GTTTTGTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
30 14 0.41
32 8 0.24
33 3 0.09
34 9 0.26
ACGTcount: A:0.20, C:0.10, G:0.04, T:0.66
Consensus pattern (29 bp):
TTGTTTTTCTTTAATTTAACACTTTTATT
Found at i:2922315 original size:67 final size:65
Alignment explanation
Indices: 2922208--2922331 Score: 144
Period size: 67 Copynumber: 1.9 Consensus size: 65
2922198 TTTTCTGAAA
* * *
2922208 TTTAATATTTTCTTCATTTATTTTATTTTTTTTTCTTTTAACATTTTTATATAATATTTTTAAAA
1 TTTAATATTTCCTTCATTTATATTATTTTTTTTTCATTT-A-ATTTTTATATAATATTTTTAAAA
2922273 AT
64 AT
* * *
2922275 TTTAATATTTCCTTC-TTTGA-ATTATTTTATTTTTGATTTAATTTTTATTTGATATTT
1 TTTAATATTTCCTTCATTT-ATATTATTTT-TTTTTCATTTAATTTTTATATAATATTT
2922332 ATTTTATTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
65 15 0.31
66 11 0.22
67 23 0.47
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.66
Consensus pattern (65 bp):
TTTAATATTTCCTTCATTTATATTATTTTTTTTTCATTTAATTTTTATATAATATTTTTAAAAAT
Found at i:2923403 original size:17 final size:16
Alignment explanation
Indices: 2923364--2923403 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
2923354 TCTCACTAAC
2923364 TTTTTTCCTTTATTTT
1 TTTTTTCCTTTATTTT
*
2923380 TTGTTTTCTTTTATTTT
1 TT-TTTTCCTTTATTTT
2923397 ATTTTTT
1 -TTTTTT
2923404 ATCCTTTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 2 0.10
17 17 0.81
18 2 0.10
ACGTcount: A:0.07, C:0.07, G:0.03, T:0.82
Consensus pattern (16 bp):
TTTTTTCCTTTATTTT
Found at i:2929493 original size:18 final size:18
Alignment explanation
Indices: 2929470--2929512 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
2929460 CTTTAGATTA
*
2929470 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
*
2929488 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
2929506 TTTATTT
1 TTTATTT
2929513 TAAAAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:2929577 original size:12 final size:11
Alignment explanation
Indices: 2929562--2929608 Score: 60
Period size: 12 Copynumber: 4.2 Consensus size: 11
2929552 CTATTATTTA
2929562 TTATTTTATCTT
1 TTATTTTA-CTT
2929574 TTATTTTA-TT
1 TTATTTTACTT
*
2929584 TTATTCTACCTT
1 TTATTTTA-CTT
2929596 TTATTTTACTT
1 TTATTTTACTT
2929607 TT
1 TT
2929609 TTTCATTCCT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 9 0.29
11 5 0.16
12 17 0.55
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATTTTACTT
Found at i:2929578 original size:22 final size:22
Alignment explanation
Indices: 2929560--2929603 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2929550 TACTATTATT
* *
2929560 TATTATTTTATCTTTTATTTTA
1 TATTATTCTACCTTTTATTTTA
*
2929582 TTTTATTCTACCTTTTATTTTA
1 TATTATTCTACCTTTTATTTTA
2929604 CTTTTTTTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.70
Consensus pattern (22 bp):
TATTATTCTACCTTTTATTTTA
Found at i:2929630 original size:23 final size:22
Alignment explanation
Indices: 2929575--2929630 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
2929565 TTTTATCTTT
* *
2929575 TATTTTATTTTATTCTACCTTT
1 TATTTTCTTTTATTCTACCTTG
* *
2929597 TATTTTACTTTTTTTCATTCCTTG
1 TATTTT-CTTTTATTC-TACCTTG
2929621 TATTTTCTTT
1 TATTTTCTTT
2929631 AAAATTTAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 6 0.21
23 11 0.39
24 11 0.39
ACGTcount: A:0.14, C:0.14, G:0.02, T:0.70
Consensus pattern (22 bp):
TATTTTCTTTTATTCTACCTTG
Found at i:2929693 original size:5 final size:5
Alignment explanation
Indices: 2929649--2929712 Score: 58
Period size: 5 Copynumber: 11.8 Consensus size: 5
2929639 ACACTTCATT
*
2929649 TTTTA TTTT- TTTTG TTTTA TCTTTA TTTTTCCA CTTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA T-TTTA -TTTT--A -TTTTA TTTTA TTTTA
2929698 TTTTA TTTTA CTTTT
1 TTTTA TTTTA -TTTT
2929713 TCTCTTTTAA
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
4 4 0.08
5 29 0.57
6 12 0.24
7 1 0.02
8 5 0.10
ACGTcount: A:0.14, C:0.08, G:0.02, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:2929720 original size:34 final size:34
Alignment explanation
Indices: 2929649--2929740 Score: 98
Period size: 34 Copynumber: 2.6 Consensus size: 34
2929639 ACACTTCATT
*
2929649 TTTTATTTTTTTTGTTTTATCTTTATTTTTCCAC
1 TTTTATTTTTTTTATTTTATCTTTATTTTTCCAC
*
2929683 TTTTATTTTATTTTATTTTAT-TTTACTTTTT-CTC
1 TTTTATTTT-TTTTATTTTATCTTTA-TTTTTCCAC
2929717 TTTTAACATTTTTTTATATTTTAT
1 TTTT---ATTTTTTT-TATTTTAT
2929741 TATTTTTCTT
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
34 19 0.38
35 15 0.30
36 3 0.06
37 13 0.26
ACGTcount: A:0.16, C:0.09, G:0.01, T:0.74
Consensus pattern (34 bp):
TTTTATTTTTTTTATTTTATCTTTATTTTTCCAC
Found at i:2929737 original size:32 final size:32
Alignment explanation
Indices: 2929692--2929753 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
2929682 CTTTTATTTT
2929692 ATTTTATTTTATTTTACTT-TTTCTCTTTTAAC
1 ATTTTATTTTATTTTA-TTATTTCTCTTTTAAC
*
2929724 ATTTT-TTTATATTTTATTATTTTTCTTTTA
1 ATTTTATTT-TATTTTATTATTTCTCTTTTA
2929754 TGAAATTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 5 0.19
32 22 0.81
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (32 bp):
ATTTTATTTTATTTTATTATTTCTCTTTTAAC
Found at i:2933624 original size:22 final size:22
Alignment explanation
Indices: 2933599--2933653 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
2933589 TACTTAGTAT
2933599 AGTATCGATACCCTAGTTTAGA
1 AGTATCGATACCCTAGTTTAGA
*
2933621 AGTATCGATACCCTAGTTTAGC
1 AGTATCGATACCCTAGTTTAGA
2933643 AGTATCGATAC
1 AGTATCGATAC
2933654 TCAGTCCAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (22 bp):
AGTATCGATACCCTAGTTTAGA
Found at i:2935230 original size:18 final size:20
Alignment explanation
Indices: 2935207--2935245 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
2935197 CTGAAATATA
2935207 ATGTTAGAAT-TG-AATTTG
1 ATGTTAGAATGTGAAATTTG
2935225 ATGTTAGAATGTGAAATTTG
1 ATGTTAGAATGTGAAATTTG
2935245 A
1 A
2935246 CCATTTTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.53
19 2 0.11
20 7 0.37
ACGTcount: A:0.36, C:0.00, G:0.23, T:0.41
Consensus pattern (20 bp):
ATGTTAGAATGTGAAATTTG
Found at i:2943432 original size:61 final size:61
Alignment explanation
Indices: 2943334--2943459 Score: 189
Period size: 61 Copynumber: 2.1 Consensus size: 61
2943324 TTCAGTTTAA
*** * * *
2943334 CACTATAGTGTATATAAAGGACACTTAGTGTGTATGGTGGGCATGACCTTATGTGTATTAT
1 CACTATAGTGTATATAAAGGACACTTAGTGCACATGGTGGACACGACCTTATGTGTATTAG
*
2943395 CACTATAGTGTATATAAAGGACACTTAGTGCACATGGTGGACACGATCTTATGTGTATTAG
1 CACTATAGTGTATATAAAGGACACTTAGTGCACATGGTGGACACGACCTTATGTGTATTAG
2943456 CACT
1 CACT
2943460 TCGGTGCATA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.33
Consensus pattern (61 bp):
CACTATAGTGTATATAAAGGACACTTAGTGCACATGGTGGACACGACCTTATGTGTATTAG
Found at i:2946654 original size:129 final size:123
Alignment explanation
Indices: 2946301--2946941 Score: 801
Period size: 129 Copynumber: 5.1 Consensus size: 123
2946291 ATATTTTAAA
* *
2946301 ATATATATTCAATAAATTAAGAAAAAATAAAAAAATATATATTTTTATAGTTAAGAATTTAAACA
1 ATATATATTCGATAAATTAAGAAAAAATAATAAAA-ATATATTTTTATAGTTAAGAATTTAAA-A
*
2946366 TA-TATTTAAAATATATATATTCTTAACTTAAATAATAAACTTGGTCTACTTT-AAACGGAAAA-
64 TATTA-TT--AA-ATATATATTCTTAACTTAAATAATAAACTTGGCCTACTTTAAAAC-GAAAAT
*
2946428 ATATTTATTCGATAAATTAAG-AAAAATAAT-AAAATATATTTTTATAGTTAAGAATTT-AAATA
1 ATATATATTCGATAAATTAAGAAAAAATAATAAAAATATATTTTTATAGTTAAGAATTTAAAATA
*
2946490 TT-TTAAATATATATTCTTAACTTAAATAATAAACTTTGCCTACTTTAAAAC-AAAAT
66 TTATTAAATATATATTCTTAACTTAAATAATAAACTTGGCCTACTTTAAAACGAAAAT
*
2946546 ATATATATTCAATAAATTAAGAAAAAATAATAAAATATATATTTTTTTATAGTTAAGAATTTAAA
1 ATATATATTCGATAAATTAAGAAAAAATAATAAAA-ATATA--TTTTTATAGTTAAGAATTTAAA
*
2946611 CATATTATATATATATATATATTCTTAACTTAAATAATAAACTTGGTCTACTTT-AAACTGAAAA
63 -ATATTAT-TA-A-ATATATATTCTTAACTTAAATAATAAACTTGGCCTACTTTAAAAC-GAAAA
2946675 -
123 T
* *
2946675 ATATTTATTCGATAAATTAAGAAAAAATAAT-AAAACATATTTTTATAGTTAAGAATTTAAATAT
1 ATATATATTCGATAAATTAAGAAAAAATAATAAAAATATATTTTTATAGTTAAGAATTTAAA-A-
* *
2946739 TTTAAAATATTTTAAATATATATTCTTAACTTAAATAATAAACTTGGCCTACTTT-AAACCAAAA
64 --T---AT-TATTAAATATATATTCTTAACTTAAATAATAAACTTGGCCTACTTTAAAACGAAAA
2946803 T
123 T
2946804 ATATATATTCGATAAATTAAGAAAAATAATAATAAAATATATATTTTTATAGTTAAGAATTT-AA
1 ATATATATTCGATAAATTAAG-AAAA-AATAATAAAA-ATATATTTTTATAGTTAAGAATTTAAA
* * *
2946868 ATATT-TTAAATATATATTCTTACCTCAAATAATAAACTTGGCCTACTTT-AAACCAAAA-
63 ATATTATTAAATATATATTCTTAACTTAAATAATAAACTTGGCCTACTTTAAAACGAAAAT
*
2946926 ATATATATACGATAAA
1 ATATATATTCGATAAA
2946942 AAAACACATA
Statistics
Matches: 465, Mismatches: 21, Indels: 61
0.85 0.04 0.11
Matches are distributed among these distances:
117 4 0.01
118 57 0.12
119 15 0.03
120 3 0.01
121 7 0.02
122 18 0.04
123 73 0.16
124 27 0.06
125 33 0.07
126 9 0.02
127 25 0.05
128 14 0.03
129 130 0.28
130 9 0.02
131 11 0.02
132 7 0.02
133 23 0.05
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.39
Consensus pattern (123 bp):
ATATATATTCGATAAATTAAGAAAAAATAATAAAAATATATTTTTATAGTTAAGAATTTAAAATA
TTATTAAATATATATTCTTAACTTAAATAATAAACTTGGCCTACTTTAAAACGAAAAT
Found at i:2946862 original size:258 final size:242
Alignment explanation
Indices: 2946301--2946941 Score: 950
Period size: 247 Copynumber: 2.6 Consensus size: 242
2946291 ATATTTTAAA
*
2946301 ATATATATTCAATAAATTAAGAAAAAATAAAAAAATATATATTTTTATAGTTAAGAATTTAAACA
1 ATATATATTCAATAAATTAAGAAAAAATAATAAAATATATATTTTTATAGTTAAGAATTTAAACA
2946366 TA-TATTTAAAATATATATATTCTTAACTTAAATAATAAACTTGGTCTACTTTAAACGGAAAAAT
66 TATTA-TT--AATATATATATTCTTAACTTAAATAATAAACTTGGTCTACTTTAAAC-GAAAAAT
*
2946430 ATTTATTCGATAAATTAAGAAAAATAATAAAATATATTTTTATAGTTAAGAATTTAAATATTTTA
127 ATTTATTCGATAAATTAAGAAAAATAATAAAACATATTTTTATAGTTAAGAATTTAAATATTTTA
*
2946495 AATATATATTCTTAACTTAAATAATAAACTTTGCCTACTTTAAAACAAAAT
192 AATATATATTCTTAACTTAAATAATAAACTTGGCCTACTTTAAAACAAAAT
2946546 ATATATATTCAATAAATTAAGAAAAAATAATAAAATATATATTTTTTTATAGTTAAGAATTTAAA
1 ATATATATTCAATAAATTAAGAAAAAATAATAAAATATATA--TTTTTATAGTTAAGAATTTAAA
2946611 CATATTATATATATATATATATTCTTAACTTAAATAATAAACTTGGTCTACTTTAAACTGAAAAA
64 CATATTAT-TA-ATATATATATTCTTAACTTAAATAATAAACTTGGTCTACTTTAAAC-GAAAAA
2946676 TATTTATTCGATAAATTAAGAAAAAATAATAAAACATATTTTTATAGTTAAGAATTTAAATATTT
126 TATTTATTCGATAAATTAAG-AAAAATAATAAAACATATTTTTATAGTTAAG-------A-A-TT
*
2946741 TAAAATATTTTAAATATATATTCTTAACTTAAATAATAAACTTGGCCTACTTTAAACCAAAAT
181 T-AAATATTTTAAATATATATTCTTAACTTAAATAATAAACTTGGCCTACTTTAAAACAAAAT
*
2946804 ATATATATTCGATAAATTAAGAAAAATAATAATAAAATATATATTTTTATAGTTAAGAATTT-AA
1 ATATATATTCAATAAATTAAG-AAAA-AATAATAAAATATATATTTTTATAGTTAAGAATTTAAA
* * * *
2946868 -ATATT-TTAA-ATATATATTCTTACCTCAAATAATAAACTTGGCCTACTTTAAACCAAAAATAT
64 CATATTATTAATATATATATTCTTAACTTAAATAATAAACTTGGTCTACTTTAAACGAAAAATAT
* *
2946930 ATATACGATAAA
129 TTATTCGATAAA
2946942 AAAACACATA
Statistics
Matches: 366, Mismatches: 12, Indels: 30
0.90 0.03 0.07
Matches are distributed among these distances:
245 40 0.11
246 1 0.00
247 99 0.27
248 33 0.09
251 18 0.05
252 41 0.11
253 1 0.00
254 2 0.01
255 2 0.01
256 6 0.02
257 5 0.01
258 98 0.27
259 4 0.01
260 16 0.04
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.39
Consensus pattern (242 bp):
ATATATATTCAATAAATTAAGAAAAAATAATAAAATATATATTTTTATAGTTAAGAATTTAAACA
TATTATTAATATATATATTCTTAACTTAAATAATAAACTTGGTCTACTTTAAACGAAAAATATTT
ATTCGATAAATTAAGAAAAATAATAAAACATATTTTTATAGTTAAGAATTTAAATATTTTAAATA
TATATTCTTAACTTAAATAATAAACTTGGCCTACTTTAAAACAAAAT
Found at i:2949503 original size:42 final size:43
Alignment explanation
Indices: 2949453--2949545 Score: 134
Period size: 42 Copynumber: 2.2 Consensus size: 43
2949443 TTTGGTAAAA
2949453 AAACGCCGCAATAGGTAACGAGATATAGCGGCGTTTGT-CCAC
1 AAACGCCGCAATAGGTAACGAGATATAGCGGCGTTTGTCCCAC
*** * *
2949495 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTAACGAGATATAGCGGCGTTTGTCCCAC
2949538 AAACGCCG
1 AAACGCCG
2949546 TAAAATGCGT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 33 0.73
43 12 0.27
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.22
Consensus pattern (43 bp):
AAACGCCGCAATAGGTAACGAGATATAGCGGCGTTTGTCCCAC
Found at i:2949567 original size:43 final size:42
Alignment explanation
Indices: 2949472--2949591 Score: 120
Period size: 43 Copynumber: 2.9 Consensus size: 42
2949462 AATAGGTAAC
* * *
2949472 GAGATATAGCGGCGTTTGTCCACAAACGCCGCAATAGGTGTT
1 GAGATATAGCGGCGTTTTTCCACAAACGCCGCAAAAGGCGTT
* * *
2949514 GAGATTTAGCGGCGTTTTTCCCACAAACGCCGTAAAATGCGTAT
1 GAGATATAGCGGCGTTTTT-CCACAAACGCCGCAAAAGGCGT-T
* * *
2949558 G-TATATAGCGGCGTTTTT--ATAAACGCCTCAAAAG
1 GAGATATAGCGGCGTTTTTCCACAAACGCCGCAAAAG
2949592 CTTAAGATAT
Statistics
Matches: 64, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
40 12 0.19
42 17 0.27
43 33 0.52
44 2 0.03
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (42 bp):
GAGATATAGCGGCGTTTTTCCACAAACGCCGCAAAAGGCGTT
Found at i:2949675 original size:42 final size:42
Alignment explanation
Indices: 2949558--2949701 Score: 125
Period size: 42 Copynumber: 3.4 Consensus size: 42
2949548 AAATGCGTAT
* *
2949558 GTATATAGCGGCG-TTTT--TATAAACGCCTCAAAAGCT-TAAG
1 GTATATAGCGGCGTTTTTCATATAAACGCCGCAAAAGATCT--G
* * * * * *
2949598 ATATTTTGCGGTGTTTTTCGGATACAAACGTCGCAAAAGATCTG
1 GTATATAGCGGCGTTTTTC--ATATAAACGCCGCAAAAGATCTG
*
2949642 GTATATAGCGGCGTTTTTCATATAAACGCCGCAAAAGGTCTG
1 GTATATAGCGGCGTTTTTCATATAAACGCCGCAAAAGATCTG
* *
2949684 GTATATAGTGGCATTTTT
1 GTATATAGCGGCGTTTTT
2949702 AGGATACAAA
Statistics
Matches: 81, Mismatches: 17, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
40 9 0.11
41 4 0.05
42 36 0.44
44 16 0.20
45 15 0.19
46 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.33
Consensus pattern (42 bp):
GTATATAGCGGCGTTTTTCATATAAACGCCGCAAAAGATCTG
Found at i:2950115 original size:42 final size:42
Alignment explanation
Indices: 2950069--2950181 Score: 120
Period size: 42 Copynumber: 2.7 Consensus size: 42
2950059 ATTCTTGACA
* * *
2950069 TCTCTGCTGATAT-GTTGCTTCTCTCTGTGTTGTCGTTGATTC
1 TCTCTG-TGATATCGATGCTTCTCTCTGTGCTGTCATTGATTC
* * *
2950111 TCTCTGTGTTGTCGATGCTTCTCTCTGTGCTGTCATTGCTTC
1 TCTCTGTGATATCGATGCTTCTCTCTGTGCTGTCATTGATTC
* * * *
2950153 TCTCTATGCTGTCAATGCTTCTCTCTGTG
1 TCTCTGTGATATCGATGCTTCTCTCTGTG
2950182 TTGCTATTGC
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
41 4 0.07
42 57 0.93
ACGTcount: A:0.07, C:0.25, G:0.20, T:0.48
Consensus pattern (42 bp):
TCTCTGTGATATCGATGCTTCTCTCTGTGCTGTCATTGATTC
Found at i:2950191 original size:42 final size:42
Alignment explanation
Indices: 2950084--2950199 Score: 153
Period size: 42 Copynumber: 2.8 Consensus size: 42
2950074 GCTGATATGT
* * * * *
2950084 TGCTTCTCTCTGTGTTGTCGTTGATTCTCTCTGTGTTGTCGA
1 TGCTTCTCTCTGTGTTGTCATTGCTTCTCTCTATGCTGTCAA
*
2950126 TGCTTCTCTCTGTGCTGTCATTGCTTCTCTCTATGCTGTCAA
1 TGCTTCTCTCTGTGTTGTCATTGCTTCTCTCTATGCTGTCAA
*
2950168 TGCTTCTCTCTGTGTTG-CTATTGCTGCTCTCT
1 TGCTTCTCTCTGTGTTGTC-ATTGCTTCTCTCT
2950200 CTACTTCCCT
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
41 1 0.02
42 64 0.98
ACGTcount: A:0.06, C:0.26, G:0.20, T:0.48
Consensus pattern (42 bp):
TGCTTCTCTCTGTGTTGTCATTGCTTCTCTCTATGCTGTCAA
Found at i:2950192 original size:21 final size:21
Alignment explanation
Indices: 2950083--2950199 Score: 139
Period size: 21 Copynumber: 5.6 Consensus size: 21
2950073 TGCTGATATG
*
2950083 TTGCTTCTCTCTGTGTTGTCG
1 TTGCTTCTCTCTGTGTTGTCA
*
2950104 TTGATTCTCTCTGTGTTGTCGA
1 TTGCTTCTCTCTGTGTTGTC-A
*
2950126 -TGCTTCTCTCTGTGCTGTCA
1 TTGCTTCTCTCTGTGTTGTCA
* *
2950146 TTGCTTCTCTCTATGCTGTCA
1 TTGCTTCTCTCTGTGTTGTCA
*
2950167 ATGCTTCTCTCTGTGTTG-CTA
1 TTGCTTCTCTCTGTGTTGTC-A
*
2950188 TTGCTGCTCTCT
1 TTGCTTCTCTCT
2950200 CTACTTCCCT
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
20 2 0.02
21 81 0.98
ACGTcount: A:0.06, C:0.26, G:0.20, T:0.49
Consensus pattern (21 bp):
TTGCTTCTCTCTGTGTTGTCA
Found at i:2952769 original size:10 final size:10
Alignment explanation
Indices: 2952754--2952778 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2952744 GGAGTATTAA
2952754 ATTTATTTTC
1 ATTTATTTTC
2952764 ATTTATTTTC
1 ATTTATTTTC
2952774 ATTTA
1 ATTTA
2952779 ATAAATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (10 bp):
ATTTATTTTC
Found at i:2953392 original size:364 final size:364
Alignment explanation
Indices: 2952472--2953540 Score: 1472
Period size: 364 Copynumber: 2.9 Consensus size: 364
2952462 TTTTTACTAT
* * * * * *
2952472 AACTATACCGGTGA-TAACTAATTATTGTC-TATTTTCATTTTGATCA-T-TTTTTAAAATTTTG
1 AACTATACCAGTGACTAA-TAACTATTG-CGCATTTTCATTTTGACCACTATTTTTGAATTTTTG
*
2952533 TCAATCAGATCATCCAACTATTTAAATGCATTCAATCAAGCCACTTGCCGCTAATATTTAACGAA
64 TCAATCAGATCATCCAACTATTTAAATGCATTCAATCAAGCCACTTCCCGCTAATATTTAACGAA
* * * * *
2952598 GAAGCTGACATGGCGGTTAAAATATTTTGATATAATTACACATTTGGCCACCGTTACTTGTATAT
129 GAAGTTGACATGGCGGTTAAAATA-TTTGGTATAATTACACATTTGGTCACTGTTACTTGAATAT
* *
2952663 TCTATCAACTTGATCCTAATTTTAAT-AATTAAAATAAATTTCACCTTCGAATCAGATTATGTCA
193 TCTATCAATTTGGTCCTAATTTTAATAAATTAAAATAAATTTCACCTTCGAATCAGATTATGTCA
* * * *
2952727 TGTGTCACCAATCTAGTGGAGTATTAAATTTATTTTCATTTATTTTCATTTAATAAATTTATTTC
258 TGTGTCACCAATCGATTGGAGTATTAAATTTATTTTAATTTAATTTCATTTAATAAATTTATTTC
* * *
2952792 CCAACAGTTAGAGGCTGACACGTGTAACCTTTTTTTAGGTTA
323 CCAACAATTAGAGGCTGACACATGTAACCTCTTTTTAGGTTA
* *
2952834 AACTATACGAGTGACTAATAACTATTGCGCCTTTTCATTTTGACCACTATTTTTGAATTTTT-TC
1 AACTATACCAGTGACTAATAACTATTGCGCATTTTCATTTTGACCACTATTTTTGAATTTTTGT-
* ** *
2952898 CAATCTGATCATCCAACTATTTAAATGTGTTCAATCAAGCCACTTCTCGCTAATATTTAACGAAG
65 CAATCAGATCATCCAACTATTTAAATGCATTCAATCAAGCCACTTCCCGCTAATATTTAACGAAG
*
2952963 AAGTTGGCATGGCGGTTAAAATATTTGGTATAATTACACATTTGGTCACTGTTACTTGAATATTC
130 AAGTTGACATGGCGGTTAAAATATTTGGTATAATTACACATTTGGTCACTGTTACTTGAATATTC
* * *
2953028 TATCAATTTGGTCCTAATTTTAATAAATTAAAATATATTTCACCTACGAATCAAATTATGTCATG
195 TATCAATTTGGTCCTAATTTTAATAAATTAAAATAAATTTCACCTTCGAATCAGATTATGTCATG
* * *
2953093 TGTCACTAATCGATTGGAGTATTAAATTTATTTTAATTTACTTTCATTTAATAAATTTATTTTCC
260 TGTCACCAATCGATTGGAGTATTAAATTTATTTTAATTTAATTTCATTTAATAAATTTATTTCCC
* * * * * *
2953158 ACCAATTATAGGGTTATACATGTCACC-CTTTTTAGGTTA
325 AACAATTAGAGGCTGACACATGTAACCTCTTTTTAGGTTA
* * * ** *
2953197 AATTATACCTGTGACTACTGGCTATTGCGCATTTTCATTTTAACCACTATTTTTGAATTTTTGTC
1 AACTATACCAGTGACTAATAACTATTGCGCATTTTCATTTTGACCACTATTTTTGAATTTTTGTC
* *
2953262 AATCAGATTATCCAACTATTTAAATGCATTCAATCAAGCCAATTCCCGCTAATATTTAACGTAA-
66 AATCAGATCATCCAACTATTTAAATGCATTCAATCAAGCCACTTCCCGCTAATATTTAACG-AAG
** * *
2953326 AAGTTGATGTGGCGGTTAACAA-AGTTTGGTATAATTACACATTTGATCACTGTTACTTGCATAT
130 AAGTTGACATGGCGGTTAA-AATA-TTTGGTATAATTACACATTTGGTCACTGTTACTTGAATAT
2953390 TCTATCAATTTGGTCCTAATTTTAATAAATTAAAATAAATTTCACCTTCGAATCAGATTATGTCA
193 TCTATCAATTTGGTCCTAATTTTAATAAATTAAAATAAATTTCACCTTCGAATCAGATTATGTCA
* * * * *
2953455 CGTGTCACCATTTGATTGGAGTATTAAATTTATATTAATTTAATTTCATTTAATAATTTTATTTC
258 TGTGTCACCAATCGATTGGAGTATTAAATTTATTTTAATTTAATTTCATTTAATAAATTTATTTC
* * *
2953520 TCAACAATCAGAGGGTGACAC
323 CCAACAATTAGAGGCTGACAC
2953541 GTGTTACCCT
Statistics
Matches: 622, Mismatches: 75, Indels: 18
0.87 0.10 0.03
Matches are distributed among these distances:
361 1 0.00
362 34 0.05
363 203 0.33
364 384 0.62
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (364 bp):
AACTATACCAGTGACTAATAACTATTGCGCATTTTCATTTTGACCACTATTTTTGAATTTTTGTC
AATCAGATCATCCAACTATTTAAATGCATTCAATCAAGCCACTTCCCGCTAATATTTAACGAAGA
AGTTGACATGGCGGTTAAAATATTTGGTATAATTACACATTTGGTCACTGTTACTTGAATATTCT
ATCAATTTGGTCCTAATTTTAATAAATTAAAATAAATTTCACCTTCGAATCAGATTATGTCATGT
GTCACCAATCGATTGGAGTATTAAATTTATTTTAATTTAATTTCATTTAATAAATTTATTTCCCA
ACAATTAGAGGCTGACACATGTAACCTCTTTTTAGGTTA
Found at i:2953871 original size:29 final size:29
Alignment explanation
Indices: 2953815--2953927 Score: 102
Period size: 29 Copynumber: 3.9 Consensus size: 29
2953805 AAAATTACAC
* ** *
2953815 ATATTTTATTCTTATCTTTGCTAAAAAAA
1 ATATATTATTCTTATCTTAACTTAAAAAA
* * *
2953844 ATATGTTATTCTTATTTTAACGTT-AAAAT
1 ATATATTATTCTTATCTTAAC-TTAAAAAA
* *
2953873 ATATCTTAGTCTTATCTTAACTTAAAAAA
1 ATATATTATTCTTATCTTAACTTAAAAAA
* * *
2953902 ATAAATTATTCTTACCTTAAATTAAA
1 ATATATTATTCTTATCTTAACTTAAA
2953928 TATTTATATT
Statistics
Matches: 67, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
28 2 0.03
29 64 0.96
30 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.46
Consensus pattern (29 bp):
ATATATTATTCTTATCTTAACTTAAAAAA
Found at i:2953983 original size:22 final size:22
Alignment explanation
Indices: 2953958--2954032 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
2953948 AATATTTTAA
2953958 ATTTAAGATAAAAATAAAATAT
1 ATTTAAGATAAAAATAAAATAT
* * *
2953980 ATTTTAATTAAGATAAAATTAAATTTT
1 A---T--TTAAGATAAAAATAAAATAT
* *
2954007 AATTAAGATAAAAATATAATAT
1 ATTTAAGATAAAAATAAAATAT
2954029 ATTT
1 ATTT
2954033 TTAAATTAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 10
0.67 0.16 0.17
Matches are distributed among these distances:
22 20 0.51
25 1 0.03
27 18 0.46
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (22 bp):
ATTTAAGATAAAAATAAAATAT
Found at i:2954006 original size:51 final size:51
Alignment explanation
Indices: 2953951--2954048 Score: 146
Period size: 49 Copynumber: 1.9 Consensus size: 51
2953941 TTCTTATAAT
*
2953951 ATTTTAAATTTAAGATAAAAATAAAATATA-TTTT-AATTAAGATAAAATTAA
1 ATTTT-AA-TTAAGATAAAAATAAAATATATTTTTAAATTAAAATAAAATTAA
*
2954002 ATTTTAATTAAGATAAAAATATAATATATTTTTAAATTAAAATAAAA
1 ATTTTAATTAAGATAAAAATAAAATATATTTTTAAATTAAAATAAAA
2954049 ATCAAATGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
49 20 0.47
50 6 0.14
51 17 0.40
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (51 bp):
ATTTTAATTAAGATAAAAATAAAATATATTTTTAAATTAAAATAAAATTAA
Found at i:2954126 original size:21 final size:21
Alignment explanation
Indices: 2954100--2954149 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 21
2954090 ATTTAAAATG
*
2954100 TTTAATTTATTTTTATTTTTA
1 TTTAATTTATTTTTATTTTCA
2954121 TTTAATTTATTTTTATTTTCA
1 TTTAATTTATTTTTATTTTCA
2954142 TCTTAATT
1 T-TTAATT
2954150 AAAAAATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 21 0.78
22 6 0.22
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTAATTTATTTTTATTTTCA
Found at i:2954240 original size:28 final size:29
Alignment explanation
Indices: 2954209--2954324 Score: 78
Period size: 28 Copynumber: 4.0 Consensus size: 29
2954199 AATAAAAATA
*
2954209 TTTAATTTAAGTAAG-GT-AAATTATATTT
1 TTTAATTTAAGTAAGACTGAAA-TATATTT
* *
2954237 TTTAAGTTAACATAAGACTGAAATATATTT
1 TTTAATTTAA-GTAAGACTGAAATATATTT
* * *
2954267 TTTAAGTTAAAGTAAGAAT--AATATATAT
1 TTTAA-TTTAAGTAAGACTGAAATATATTT
* * * *
2954295 TTTAAGTTAAGATAATAATAAAATATATTT
1 TTTAATTTAAG-TAAGACTGAAATATATTT
2954325 AATTATTTAA
Statistics
Matches: 69, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
27 4 0.06
28 28 0.41
29 4 0.06
30 27 0.39
31 6 0.09
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.43
Consensus pattern (29 bp):
TTTAATTTAAGTAAGACTGAAATATATTT
Found at i:2954266 original size:30 final size:28
Alignment explanation
Indices: 2954225--2954324 Score: 112
Period size: 30 Copynumber: 3.4 Consensus size: 28
2954215 TTAAGTAAGG
*
2954225 TAAATTATATTTTTTAAGTTAACATAAGAC
1 TAAA-TATATTTTTTAAGTTAA-ATAAGAA
2954255 TGAAATATATTTTTTAAGTTAAAGTAAGAA
1 T-AAATATATTTTTTAAGTTAAA-TAAGAA
* *
2954285 T-AATATATATTTTAAGTTAAGATAATAA
1 TAAATATATTTTTTAAGTTAA-ATAAGAA
2954313 TAAAATATATTT
1 T-AAATATATTT
2954325 AATTATTTAA
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
28 24 0.39
29 2 0.03
30 32 0.52
31 3 0.05
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (28 bp):
TAAATATATTTTTTAAGTTAAATAAGAA
Found at i:2954345 original size:58 final size:58
Alignment explanation
Indices: 2954230--2954357 Score: 143
Period size: 58 Copynumber: 2.2 Consensus size: 58
2954220 TAAGGTAAAT
* * * * *
2954230 TATATTTTTTAAGTTAACATAAGACTGAAATATATTTTTTAAGTTAAAGTAAGAATAA
1 TATATATTTTAAGTTAACATAAGAATAAAATATATTTATTAAGTTAAAGTAAAAATAA
* * *
2954288 TATATATTTTAAGTTAAGATAATAATAAAATATATTTAATT-A-TTTAAGATAAAAATAA
1 TATATATTTTAAGTTAACATAAGAATAAAATATATTT-ATTAAGTTAAAG-TAAAAATAA
*
2954346 TATATACTTTAA
1 TATATATTTTAA
2954358 ATGTTAAAAT
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
57 5 0.08
58 52 0.88
59 2 0.03
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.42
Consensus pattern (58 bp):
TATATATTTTAAGTTAACATAAGAATAAAATATATTTATTAAGTTAAAGTAAAAATAA
Found at i:2959467 original size:19 final size:19
Alignment explanation
Indices: 2959439--2959504 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
2959429 GGTATTTTAG
*
2959439 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
* *
2959458 TTTAATTAGGATTTAGAAT
1 TTTAATTAGGTTTTAGTAT
* *
2959477 ATTATATTA-TTTTTAAGTAT
1 TTTA-ATTAGGTTTT-AGTAT
2959497 TTTAATTA
1 TTTAATTA
2959505 AGACGTTTTA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 26 0.70
20 11 0.30
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.55
Consensus pattern (19 bp):
TTTAATTAGGTTTTAGTAT
Found at i:2960097 original size:4 final size:4
Alignment explanation
Indices: 2960088--2960133 Score: 60
Period size: 4 Copynumber: 12.0 Consensus size: 4
2960078 CTCAATCTGT
* *
2960088 TTTA TTTA TTTA TTTA TTTA TTTA TTTA ATTA -TTA TCT- TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
2960134 AAAAATAACT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
3 5 0.14
4 32 0.86
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:2960236 original size:41 final size:42
Alignment explanation
Indices: 2960152--2960236 Score: 95
Period size: 41 Copynumber: 2.0 Consensus size: 42
2960142 CTTTTAAAAA
* *
2960152 TCCCTTTTTATTTTAATACTATTATTTATTATTTTATTATTT
1 TCCCTTTTTATTTTAATAATATTATTTATTATTTTAATATTT
* *
2960194 TCCC-TTTTATTTATTATAATA-TATTTATT-TTATTAATCTTT
1 TCCCTTTTTATTT-TAATAATATTATTTATTATT-TTAATATTT
2960235 TC
1 TC
2960237 AACTTTATCT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
40 2 0.05
41 25 0.68
42 10 0.27
ACGTcount: A:0.25, C:0.11, G:0.00, T:0.65
Consensus pattern (42 bp):
TCCCTTTTTATTTTAATAATATTATTTATTATTTTAATATTT
Found at i:2961752 original size:18 final size:18
Alignment explanation
Indices: 2961729--2961771 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
2961719 TGCCCTGATC
2961729 ATGTTGAAAGAATTAATT
1 ATGTTGAAAGAATTAATT
2961747 ATGTTGAAAGAATTAATT
1 ATGTTGAAAGAATTAATT
2961765 ATGTTGA
1 ATGTTGA
2961772 TTTTATAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.40
Consensus pattern (18 bp):
ATGTTGAAAGAATTAATT
Found at i:2964926 original size:5 final size:5
Alignment explanation
Indices: 2964897--2964962 Score: 53
Period size: 5 Copynumber: 12.6 Consensus size: 5
2964887 AGGTAACCCA
* ** *
2964897 TTTAGT TTTAT TTCCAT TTTA- TTTAT TTTAT TTTAT TTTAT CATAT GCTTAAT
1 TTTA-T TTTAT TT-TAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT --TTTAT
2964950 TTTAT TTTAT TTT
1 TTTAT TTTAT TTT
2964963 TCTCTGAACA
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
4 4 0.08
5 34 0.71
6 8 0.17
7 2 0.04
ACGTcount: A:0.21, C:0.06, G:0.03, T:0.70
Consensus pattern (5 bp):
TTTAT
Found at i:2966687 original size:19 final size:19
Alignment explanation
Indices: 2966659--2966720 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
2966649 GGTATTTTAG
*
2966659 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
* *
2966678 TTTAATTAGGATTTAGAAT
1 TTTAATTAGGTTTTAGTAT
* *
2966697 ATTATATTA-TTTTTAGGTAT
1 TTTA-ATTAGGTTTTA-GTAT
2966717 TTTA
1 TTTA
2966721 GTTTAAATAG
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
19 23 0.70
20 10 0.30
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (19 bp):
TTTAATTAGGTTTTAGTAT
Done.