Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008925.1 Hibiscus syriacus cultivar Beakdansim tig00112230_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: 2702387
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 11
Found at i:1945347 original size:81 final size:81
Alignment explanation
Indices: 1945208--1945457 Score: 349
Period size: 81 Copynumber: 3.1 Consensus size: 81
1945198 TTTTCTAAAA
* * * * *
1945208 TAAAAGAATAATGGCCTAGTTGTGCATTTGGCAGAAATGTGTCAATTATGCCAATTAGATAAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAAGTGTCAATTATGCCAGTTAGATGAAAG
1945273 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * *
1945289 TAAAAGATTAATGGCCTAGCTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAAGTGTCAATTATGCCAGTTAGATGAAAG
1945354 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * *
1945370 TAAAATATTAATGACCTAGCTGTGCATTTGGCAGAAAAGTGTCAATCATG-CAGGTTAGATGAAA
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAAGTGTCAATTATGCCA-GTTAGATGAAA
* * * *
1945434 GGCTAAATGCCCTTGGG
65 GGTTAAATACCTTTGAG
1945451 TAAAAGA
1 TAAAAGA
1945458 CTAAAGGAAT
Statistics
Matches: 150, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
80 2 0.01
81 148 0.99
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.28
Consensus pattern (81 bp):
TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAAGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:1945798 original size:843 final size:841
Alignment explanation
Indices: 1944142--1945827 Score: 2691
Period size: 843 Copynumber: 2.0 Consensus size: 841
1944132 ATAGGGACTC
* *
1944142 ATCTAATCCTTATGGATGATACGAATTAGTTAAAAAAACCTAAGAAATTCATAATAAGTTTTTGA
1 ATCTAATCCTTATGGATGATACGAATTAGTTAAAAAAACCTAAGAAATACAAAATAAGTTTTTGA
* *
1944207 ATTTATGTATTGGTAGTGGGTGTGTAACCCATATAAATTATAGTAATGTTAAGGGAATGACTGTT
66 ATTTATATATTGGTAGTGGGTGTGCAACCCATATAAATTATAGTAATGTTAAGGGAATGACTGTT
* *
1944272 TTGGCACTATAGGTGTAAACTATAGAATTTTCAATGAAATTAAATAGTTAATTGATAATATGAAT
131 TTGGCACTACAGGAGTAAACTATAGAATTTTCAATGAAATTAAATAGTTAATTGATAATATGAAT
* *
1944337 AATTATTAGAGTAGAATCTGTTCTAAAATAAAAGATTAATGGCCTAACTATGCATTTGGTAGAAA
196 AATTATTAGAGTAGAATCTGTTCTAAAATAAAAGAATAATGGCCTAACTATGCATTTGGCAGAAA
* * ** *
1944402 TTTGTCAATTATGCCAGTTAGATGGAAGGTTAAACACCTTTGAGTAAAAGATTAATGGCCTAGTT
261 TGTGTCAATTATGCCAATTAGATAAAAGGTTAAACACCTTTGAGTAAAAGATTAATGGCCTAGCT
* * * *
1944467 GTGCATTTGGCATAAAGATGTCAATTATGTCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAA
326 GTGCAATTGACAGAAAGATGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAA
** * *
1944532 GATTAAGGTTCTAGCTGTGCATTTGGCAAAAAAATGTCAATCATGCAGGTTAGATGAAAGGTTGA
391 GATTAAGGACCTAGCTGTGCATTTGGCAAAAAAATGTCAATCATGCAGGTTAGATGAAAGGCTAA
* *
1944597 ATGCCTTCGGGTAAAAGACTAAAGGAATTATAATGCATTTTGATATAAATGGTGCATAAGCGGTA
456 ATGCCTTCGGGTAAAAGACTAAAGGAATTATAATGCATTTTGATATAAACGGTGCATAAGCGATA
*
1944662 TGAAAGGATGTCATATATATATAATGTACAACAATGCATAATTGGTATGAATGGATGTCATAAAG
521 TGAAAGGATGTCATATATATATAATGTACAACAATACATAATTGGTATGAATGGATGTCATAAAG
1944727 AAAAACGTAAACAATACATAATGGGCATGAAAGGATGCCCGAAATGAAAATACAAAATGGTGCGT
586 AAAAACGTAAACAATACATAATGGGCATGAAAGGATGCCCGAAATGAAAATACAAAATGGTGCGT
* * *
1944792 TAACAGTATTTAAGGTGCCGCCCATGATGATTATAAAAGATACATGATCAATTGGCACTTTGGTG
651 TAACAATATTTAAGGTGCCACCCATGATGATTATAAAAAATACATGATCAATTGGCACTTTGGTG
*
1944857 CAATACATGCATAGTATTTTCTCATTTAATGTACACAGGGAAAATAAAGAATAATGGAGAAAAAT
716 CAATACATGCATACTATTTTCTCATTTAATGTACACAGGGAAAATAAAGAATAATGGAGAAAAAT
* *
1944922 ATACAGAAGGATATGTATACTTGGCCTACTAAGAATAA-TTCTGATAATTGTATGAAAACATT
781 ATACAAAAGGATAGGTATACTTGGCCTACTAAGAATAATTTC-GATAATTGTATGAAAA-ATT
1944984 ATCTAATCCTTATGGATGATACGAATTAGTTCAAAAAAACCTAAGAAATACAAAATAAGTTTTTG
1 ATCTAATCCTTATGGATGATACGAATTAGTT-AAAAAAACCTAAGAAATACAAAATAAGTTTTTG
* * * **
1945049 AATTTCTATATTGGTAGTGGGTGTGCAACCTATGTAAATTATAGTAATGTTTGGGGAATGACTGT
65 AATTTATATATTGGTAGTGGGTGTGCAACCCATATAAATTATAGTAATGTTAAGGGAATGACTGT
* *
1945114 TTTGGCACTACATGAGTAAACTATGGAATTTAT-AATGAAATTAAATAGTTAATTGATAATATGA
130 TTTGGCACTACAGGAGTAAACTATAGAATTT-TCAATGAAATTAAATAGTTAATTGATAATATGA
* * ** *
1945178 ATAATTATTAGAGTAGGATCTTTTCTAAAATAAAAGAATAATGGCCTAGTTGTGCATTTGGCAGA
194 ATAATTATTAGAGTAGAATCTGTTCTAAAATAAAAGAATAATGGCCTAACTATGCATTTGGCAGA
*
1945243 AATGTGTCAATTATGCCAATTAGATAAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCTAG
259 AATGTGTCAATTATGCCAATTAGATAAAAGGTTAAACACCTTTGAGTAAAAGATTAATGGCCTAG
*
1945308 CTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAA
324 CTGTGCAATTGACAGAAAGATGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAA
* * * *
1945373 AATATTAATGACCTAGCTGTGCATTTGGCAGAAAAGTGTCAATCATGCAGGTTAGATGAAAGGCT
389 AAGATTAAGGACCTAGCTGTGCATTTGGCAAAAAAATGTCAATCATGCAGGTTAGATGAAAGGCT
1945438 AAATGCCCTT-GGGTAAAAGACTAAAGGAATTATAATGCATTTTGATATAAACGGTGCATAAGCG
454 AAATG-CCTTCGGGTAAAAGACTAAAGGAATTATAATGCATTTTGATATAAACGGTGCATAAGCG
*
1945502 ATATGAAAGGATGTCATATTTATATAATGTACAACAATACATAATTGGTATGAATGGATGTCATA
518 ATATGAAAGGATGTCATATATATATAATGTACAACAATACATAATTGGTATGAATGGATGTCATA
* * * *
1945567 AAGGACAATGTAAATAATACATAATGGGCATGAAAGGATGCTCC-AAATGAAAATACAAAATGGT
583 AAGAAAAACGTAAACAATACATAATGGGCATGAAAGGATGC-CCGAAATGAAAATACAAAATGGT
* * *
1945631 GTGTTAACAATATTTAAGGTGTCACCCATGATGATTATAAAAAATACATGATCAATTGGCATTTT
647 GCGTTAACAATATTTAAGGTGCCACCCATGATGATTATAAAAAATACATGATCAATTGGCACTTT
** * * *
1945696 GGTGCAATACATGTGTTCTATTTTTCTCATTTAATGTACACAGGGCAAATAAAGAATAATGG-GG
712 GGTGCAATACATGCATACTA-TTTTCTCATTTAATGTACACAGGGAAAATAAAGAATAATGGAGA
* *
1945760 AAAATATACAAAAGGATAGGTAT-GTTGGGCCTACTAAGAATAATTTCGATAATTGTGTGAAAAA
776 AAAATATACAAAAGGATAGGTATACTT-GGCCTACTAAGAATAATTTCGATAATTGTATGAAAAA
1945824 TT
840 TT
1945826 AT
1 AT
1945828 GGTTTAATTG
Statistics
Matches: 774, Mismatches: 63, Indels: 14
0.91 0.07 0.02
Matches are distributed among these distances:
842 38 0.05
843 686 0.89
844 50 0.06
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (841 bp):
ATCTAATCCTTATGGATGATACGAATTAGTTAAAAAAACCTAAGAAATACAAAATAAGTTTTTGA
ATTTATATATTGGTAGTGGGTGTGCAACCCATATAAATTATAGTAATGTTAAGGGAATGACTGTT
TTGGCACTACAGGAGTAAACTATAGAATTTTCAATGAAATTAAATAGTTAATTGATAATATGAAT
AATTATTAGAGTAGAATCTGTTCTAAAATAAAAGAATAATGGCCTAACTATGCATTTGGCAGAAA
TGTGTCAATTATGCCAATTAGATAAAAGGTTAAACACCTTTGAGTAAAAGATTAATGGCCTAGCT
GTGCAATTGACAGAAAGATGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAA
GATTAAGGACCTAGCTGTGCATTTGGCAAAAAAATGTCAATCATGCAGGTTAGATGAAAGGCTAA
ATGCCTTCGGGTAAAAGACTAAAGGAATTATAATGCATTTTGATATAAACGGTGCATAAGCGATA
TGAAAGGATGTCATATATATATAATGTACAACAATACATAATTGGTATGAATGGATGTCATAAAG
AAAAACGTAAACAATACATAATGGGCATGAAAGGATGCCCGAAATGAAAATACAAAATGGTGCGT
TAACAATATTTAAGGTGCCACCCATGATGATTATAAAAAATACATGATCAATTGGCACTTTGGTG
CAATACATGCATACTATTTTCTCATTTAATGTACACAGGGAAAATAAAGAATAATGGAGAAAAAT
ATACAAAAGGATAGGTATACTTGGCCTACTAAGAATAATTTCGATAATTGTATGAAAAATT
Found at i:1950019 original size:14 final size:11
Alignment explanation
Indices: 1949991--1950032 Score: 50
Period size: 10 Copynumber: 3.6 Consensus size: 11
1949981 CCTCTCACTG
1949991 TTTCTTTTCAC
1 TTTCTTTTCAC
1950002 TTTCTTCTTCATC
1 TTTCTT-TTCA-C
1950015 TTTTCTTTT-AC
1 -TTTCTTTTCAC
1950026 TTTCTTT
1 TTTCTTT
1950033 AAGTTTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
10 7 0.25
11 7 0.25
12 5 0.18
13 3 0.11
14 6 0.21
ACGTcount: A:0.07, C:0.24, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTCTTTTCAC
Found at i:1958190 original size:24 final size:24
Alignment explanation
Indices: 1958162--1958209 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
1958152 AATTCTACTT
1958162 AAGGCAAAGGCTTTTCTAATGATC
1 AAGGCAAAGGCTTTTCTAATGATC
*
1958186 AAGGCAAATGCTTTTCTAATGATC
1 AAGGCAAAGGCTTTTCTAATGATC
1958210 TCTTAAATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (24 bp):
AAGGCAAAGGCTTTTCTAATGATC
Found at i:1959726 original size:137 final size:137
Alignment explanation
Indices: 1959476--1959751 Score: 403
Period size: 137 Copynumber: 2.0 Consensus size: 137
1959466 AATAAAAGGA
*
1959476 ATATCTTTACTTAAAAGCTTGGTTAGTGGTAACGCCATCATCAAAAAGTTCTTCACGGACCTTCG
1 ATATCTTTACTTAAAAGCTTGGTTAGTGGTAACGCCATCATCAAAAAGTTCTTCACGAACCTTCG
* * **
1959541 ATAGTAATCAGCGAGTCTTAAGAAACTCTAAACTTTTGAGACATTCTTTGGGGGTTTCCAATCCA
66 ATAGTAATCAACAAGTCCCAAGAAACTCTAAACTTTTGAGACATTCTTTGGGGGTTTCCAATCCA
1959606 CTATAGC
131 CTATAGC
* * * **
1959613 ATATCTTTCCTTAAAAGCTTGGTTAGTGG-CACGCTATCATCGAAAAAGTTCTTCATTAACCTTC
1 ATATCTTTACTTAAAAGCTTGGTTAGTGGTAACGCCATCATC-AAAAAGTTCTTCACGAACCTTC
* *
1959677 GATAGTAATCAACAAGTCCCAAGAAACTTTAAACTTTTGAGATGA-TCTTTGGGGGTTTCCAATC
65 GATAGTAATCAACAAGTCCCAAGAAACTCTAAACTTTTGAGA-CATTCTTTGGGGGTTTCCAATC
*
1959741 CACTATGGC
129 CACTATAGC
1959750 AT
1 AT
1959752 GAATTTTCTT
Statistics
Matches: 124, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
136 10 0.08
137 113 0.91
138 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (137 bp):
ATATCTTTACTTAAAAGCTTGGTTAGTGGTAACGCCATCATCAAAAAGTTCTTCACGAACCTTCG
ATAGTAATCAACAAGTCCCAAGAAACTCTAAACTTTTGAGACATTCTTTGGGGGTTTCCAATCCA
CTATAGC
Found at i:1970923 original size:29 final size:30
Alignment explanation
Indices: 1970875--1970932 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
1970865 ACTTAGATCC
**
1970875 TAAACTTTCTAAATTTTATACTTTAATCAT
1 TAAACTTTCTAAAACTTATACTTTAATCAT
* *
1970905 TAAACTTTC-AAAACTTATATTTTTATCA
1 TAAACTTTCTAAAACTTATACTTTAATCA
1970933 CTAATCAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.48
Consensus pattern (30 bp):
TAAACTTTCTAAAACTTATACTTTAATCAT
Found at i:1971119 original size:15 final size:17
Alignment explanation
Indices: 1971089--1971126 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1971079 AAATTCGTAA
1971089 GCATGAAAAAATATATT
1 GCATGAAAAAATATATT
1971106 GCATGAAAAAATATATT
1 GCATGAAAAAATATATT
1971123 GCAT
1 GCAT
1971127 TCATTTACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.50, C:0.08, G:0.13, T:0.29
Consensus pattern (17 bp):
GCATGAAAAAATATATT
Found at i:1972146 original size:3 final size:3
Alignment explanation
Indices: 1972138--1972187 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
1972128 GATATGATAT
1972138 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1972185 TTA
1 TTA
1972188 ACATATGTGC
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1972353 original size:2 final size:2
Alignment explanation
Indices: 1972334--1972402 Score: 95
Period size: 2 Copynumber: 34.5 Consensus size: 2
1972324 CGAAATAAAC
* * *
1972334 AT AT AT TT AC AT AT -T AT AT AT ACT AC AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
1972376 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 A
1972403 AGTTTTATTA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
1 1 0.02
2 56 0.95
3 2 0.03
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1972907 original size:19 final size:20
Alignment explanation
Indices: 1972869--1972911 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
1972859 TCTTACATAA
*
1972869 TATTTTATATATATGTATTT
1 TATTTTATATATACGTATTT
*
1972889 TATTTTAT-TTTACGTATTT
1 TATTTTATATATACGTATTT
1972908 TATT
1 TATT
1972912 AAGCACCGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (20 bp):
TATTTTATATATACGTATTT
Found at i:1975221 original size:30 final size:30
Alignment explanation
Indices: 1975185--1975248 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
1975175 GAAGGACCTG
* *
1975185 TCCAGAGGTTACAAAGAACCCCGGTAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
* * *
1975215 TCCAGAGGTCATAAAGATCCTCGGCAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
1975245 TCCA
1 TCCA
1975249 TATGTTCCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGAACCCCGGCAACTA
Found at i:1979413 original size:30 final size:30
Alignment explanation
Indices: 1979377--1979440 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
1979367 GAAGGACCTG
* *
1979377 TCCAGAGGTTACAAAGAACCCCGGTAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
* * *
1979407 TCCAGAGGTCATAAAGATCCTCGGCAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
1979437 TCCA
1 TCCA
1979441 TATGTTCCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGAACCCCGGCAACTA
Found at i:1980250 original size:64 final size:64
Alignment explanation
Indices: 1980112--1980273 Score: 179
Period size: 64 Copynumber: 2.5 Consensus size: 64
1980102 TCTTTTAATG
* * * *
1980112 AAGGTATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTTGTATTATCAC
1 AAGG-ATGCATCGATGCACTACTTATGCATCGATGCATAAAATGCATTCGATGTTGAATTATCAA
* * *
1980177 TAGGATGCATCGATGCA-TGACTTATGCATCGATGCACT-AATTGCATTCGATGTTTGAATT-TT
1 AAGGATGCATCGATGCACT-ACTTATGCATCGATGCA-TAAAATGCATTCGATG-TTGAATTATC
1980239 AA
63 AA
*
1980241 AA-GAGTGCATCGATGCACTACCTATGCATCGAT
1 AAGGA-TGCATCGATGCACTACTTATGCATCGAT
1980274 ACACCTTCAA
Statistics
Matches: 83, Mismatches: 9, Indels: 11
0.81 0.09 0.11
Matches are distributed among these distances:
63 3 0.04
64 69 0.83
65 11 0.13
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (64 bp):
AAGGATGCATCGATGCACTACTTATGCATCGATGCATAAAATGCATTCGATGTTGAATTATCAA
Found at i:1985233 original size:37 final size:35
Alignment explanation
Indices: 1985192--1985278 Score: 104
Period size: 36 Copynumber: 2.4 Consensus size: 35
1985182 ACAAGGGGTC
*
1985192 GTCTCTCTTGAGACTAATTTACTC-AAAACATAGTTTT
1 GTCTCTCTTGAGAC-AATTT-CTCTAAAACA-AATTTT
* *
1985229 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTT
1 GTCTCTCTTGAGACAATTTCTC-TAAAACAAATTTT
1985265 GTCTCTCTTGAGAC
1 GTCTCTCTTGAGAC
1985279 GGTTTCCCTT
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
35 3 0.07
36 23 0.51
37 19 0.42
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (35 bp):
GTCTCTCTTGAGACAATTTCTCTAAAACAAATTTT
Found at i:1985272 original size:36 final size:36
Alignment explanation
Indices: 1985225--1985296 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
1985215 CAAAACATAG
*
1985225 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
1985261 TTTTGTCTCTCTTGAGACGGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1985297 AACTTTGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.40
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:1985358 original size:35 final size:35
Alignment explanation
Indices: 1985311--1985380 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 35
1985301 TTGAATTTGT
*
1985311 TTTCCTTGAAACAAAGTTT-TATCTCTTGAGACAA
1 TTTCCTTAAAACAAAGTTTGTATCTCTTGAGACAA
* *
1985345 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAA
1 TTTC-CTTAAAACAAAGTTTGTATCTCTTGAGACAA
1985381 ATTTTGTCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 4 0.13
35 13 0.42
36 14 0.45
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (35 bp):
TTTCCTTAAAACAAAGTTTGTATCTCTTGAGACAA
Found at i:1985374 original size:36 final size:36
Alignment explanation
Indices: 1985311--1985379 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 36
1985301 TTGAATTTGT
* * *
1985311 TTTC-CTTGAAACAAAGTTT-TATCTCTTGAGACAA
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
1985345 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACA
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
1985380 AATTTTGTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 4 0.13
35 13 0.43
36 13 0.43
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.41
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:1985380 original size:36 final size:36
Alignment explanation
Indices: 1985368--1985555 Score: 178
Period size: 36 Copynumber: 5.4 Consensus size: 36
1985358 AAATTTTGTC
*
1985368 TCTCTTGAGACAAATTTTGTCTCTCTTGAGACAGTT
1 TCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTT
* **
1985404 TCCCTTGAAACAAAATATTTGAATCT-TT-------TT
1 TCTCTTGAAAC-AAAT-TTTGTCTCTCTTGAGACAGTT
* *
1985434 TC-CTTTAAACAAATTTCGTCTCTCTTGAGACAGTT
1 TCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTT
* * *
1985469 TCTTTTAAAACTAAATTTTGTCTCTCTTGAGACATTT
1 TCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTT
* * *
1985506 TCTCGTAAAACAAATTTTGTCTCTCTTGAGACAATT
1 TCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTT
1985542 TCTCTTGAAACAAA
1 TCTCTTGAAACAAA
1985556 ATCTCTGAAT
Statistics
Matches: 123, Mismatches: 17, Indels: 24
0.75 0.10 0.15
Matches are distributed among these distances:
27 6 0.05
28 6 0.05
29 7 0.06
30 4 0.03
35 4 0.03
36 51 0.41
37 38 0.31
38 7 0.06
ACGTcount: A:0.29, C:0.19, G:0.11, T:0.41
Consensus pattern (36 bp):
TCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTT
Found at i:1985395 original size:21 final size:21
Alignment explanation
Indices: 1985347--1985400 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
1985337 TGAGACAATT
* *
1985347 TCTCTTAAAACAAATTTTGTC
1 TCTCTTGAGACAAATTTTGTC
1985368 TCTCTTGAGACAAATTTTGTC
1 TCTCTTGAGACAAATTTTGTC
1985389 TCTCTTGAGACA
1 TCTCTTGAGACA
1985401 GTTTCCCTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.41
Consensus pattern (21 bp):
TCTCTTGAGACAAATTTTGTC
Found at i:1985493 original size:121 final size:122
Alignment explanation
Indices: 1985247--1985641 Score: 440
Period size: 138 Copynumber: 3.1 Consensus size: 122
1985237 TGAGACAGTT
* *
1985247 TCTCTTGAAACAAATTTTGTCTCTCTTGAGACGGTTTCCCTTGAAACAAAA-ACTTTGAAT-TTG
1 TCTCTTGAGACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATA-TTTGAATCTT-
* * *
1985310 TTTTCCTTGAAACAAAGTTT--TATCTCTTGAGACAATTTCTCTTAAAAC-AAATTTTGTC
64 TTTTCCTTGAAACAAA-TTTCGTCTCTCTTGAGACAGTTTCTTTTAAAACTAAATTTTG-C
1985368 TCTCTTGAGACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATCTTTT
1 TCTCTTGAGACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATCTTTT
*
1985433 TTCCTTTAAACAAATTTCGTCTCTCTTGAGACAGTTTCTTTTAAAACTAAATTTTGTC
66 TTCCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCTTTTAAAACTAAATTTTG-C
* *
1985491 TCTCTTGAGACATTTTCTCGTAAAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAA
1 TCTCTT--G--A-------G----ACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * * * **
1985556 ATCTCTGAATCTATTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAA
51 ATATTTGAATCTTTTTTCCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCTTTTAAAACTAA
1985621 ATTTTGTC
116 ATTTTG-C
1985629 TCTCTTGAGACAA
1 TCTCTTGAGACAA
1985642 TTTCCCTTGA
Statistics
Matches: 239, Mismatches: 15, Indels: 38
0.82 0.05 0.13
Matches are distributed among these distances:
120 3 0.01
121 71 0.30
122 28 0.12
123 20 0.08
125 1 0.00
127 2 0.01
134 2 0.01
136 1 0.00
138 111 0.46
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.41
Consensus pattern (122 bp):
TCTCTTGAGACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATCTTTT
TTCCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCTTTTAAAACTAAATTTTGC
Found at i:1985537 original size:138 final size:138
Alignment explanation
Indices: 1985377--1985645 Score: 448
Period size: 138 Copynumber: 1.9 Consensus size: 138
1985367 CTCTCTTGAG
* * * *
1985377 ACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATCTTTTTTCCTTTAA
1 ACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAATATCTGAATCTATTTTCCTTGAA
* *
1985442 ACAAATTTCGTCTCTCTTGAGACAGTTTCTTTTAAAACTAAATTTTGTCTCTCTTGAGACATTTT
66 ACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTAAAACTAAATTTTGTCTCTCTTGAGACAATTT
1985507 CTCGTAAA
131 CTCGTAAA
* *
1985515 ACAAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAAATCTCTGAATCTATTTTCCTTGAA
1 ACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAATATCTGAATCTATTTTCCTTGAA
**
1985580 ACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAATTTTGTCTCTCTTGAGACAATTT
66 ACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTAAAACTAAATTTTGTCTCTCTTGAGACAATTT
1985645 C
131 C
1985646 CCTTGAAACA
Statistics
Matches: 121, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
138 121 1.00
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.42
Consensus pattern (138 bp):
ACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAATATCTGAATCTATTTTCCTTGAA
ACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTAAAACTAAATTTTGTCTCTCTTGAGACAATTT
CTCGTAAA
Found at i:1985656 original size:102 final size:101
Alignment explanation
Indices: 1985476--1985712 Score: 316
Period size: 102 Copynumber: 2.3 Consensus size: 101
1985466 GTTTCTTTTA
* *
1985476 AAACTAAATTTTGTCTCTCTTGAGACATTTTCTCGTAAAACAAATTTTGTCTCTCTTGAGACAAT
1 AAAC-AAATTTTGTCTCACTTGAGACAGTTTCTCGTAAAACAAATTTTGTCTCTCTTGAGACAAT
*
1985541 TTCTCTTGAAACAAAATCTCTGAATCTATTTTCC-TT
65 TTCCCTTGAAACAAAATCTCTGAATCTATTTTCCATT
* * ** **
1985577 GAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAATTTTGTCTCTCTTGAGACAA
1 -AAACAAATTTTGTCTCACTTGAGACAGTTTCTCGTAAAAC-AAATTTTGTCTCTCTTGAGACAA
* *
1985642 TTTCCCTTGAAACAAAATCTTTGAATCTGTTTTCCATT
64 TTTCCCTTGAAACAAAATCTCTGAATCTATTTTCCATT
*
1985680 AAACAAATTTTTTCTCACTCT-AGACAGTTTCTC
1 AAACAAATTTTGTCTCACT-TGAGACAGTTTCTC
1985713 TTGAAACACA
Statistics
Matches: 118, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
101 29 0.25
102 86 0.73
103 3 0.03
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.41
Consensus pattern (101 bp):
AAACAAATTTTGTCTCACTTGAGACAGTTTCTCGTAAAACAAATTTTGTCTCTCTTGAGACAATT
TCCCTTGAAACAAAATCTCTGAATCTATTTTCCATT
Found at i:1986699 original size:17 final size:18
Alignment explanation
Indices: 1986658--1986708 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
1986648 TTATTTATGC
* *
1986658 TATATTATATTACATCTT
1 TATATTATTTTATATCTT
1986676 TATTATTATTTTATAT-TT
1 TA-TATTATTTTATATCTT
1986694 TATATT-TTTGTATAT
1 TATATTATTT-TATAT
1986709 ATATATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 3 0.10
17 9 0.31
18 6 0.21
19 11 0.38
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (18 bp):
TATATTATTTTATATCTT
Found at i:1989210 original size:22 final size:21
Alignment explanation
Indices: 1989160--1989212 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1989150 AAAGAAGGGT
1989160 AGTATCGATACTCCTAAACCA
1 AGTATCGATACTCCTAAACCA
* * *
1989181 AGTATCGATACTTCTATACTA
1 AGTATCGATACTCCTAAACCA
1989202 ATGTATCGATA
1 A-GTATCGATA
1989213 ACAAATTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 19 0.68
22 9 0.32
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.32
Consensus pattern (21 bp):
AGTATCGATACTCCTAAACCA
Found at i:1993133 original size:25 final size:25
Alignment explanation
Indices: 1993099--1993149 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
1993089 CCTGATAGGA
* *
1993099 TAACTTAGCGAAGACCGTGGGAGGG
1 TAACTTAGCGAAGACCCTAGGAGGG
1993124 TAACTTAGCGAAGACCCTAGGAGGG
1 TAACTTAGCGAAGACCCTAGGAGGG
1993149 T
1 T
1993150 CGACTGCAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.29, C:0.18, G:0.35, T:0.18
Consensus pattern (25 bp):
TAACTTAGCGAAGACCCTAGGAGGG
Found at i:1994971 original size:20 final size:20
Alignment explanation
Indices: 1994942--1994979 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1994932 TAGCATTACT
1994942 AACCTCTGGGTACCGATACC
1 AACCTCTGGGTACCGATACC
* *
1994962 AACCTTTGGGTATCGATA
1 AACCTCTGGGTACCGATA
1994980 TTAACTGGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (20 bp):
AACCTCTGGGTACCGATACC
Found at i:1996669 original size:12 final size:12
Alignment explanation
Indices: 1996654--1996678 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1996644 CATTAAATAA
1996654 GCTTTTAACGTT
1 GCTTTTAACGTT
1996666 GCTTTTAACGTT
1 GCTTTTAACGTT
1996678 G
1 G
1996679 TACGAATCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.16, G:0.20, T:0.48
Consensus pattern (12 bp):
GCTTTTAACGTT
Found at i:1997043 original size:12 final size:12
Alignment explanation
Indices: 1997026--1997052 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1997016 TTGAATTTTT
1997026 TTAAAAAAATTA
1 TTAAAAAAATTA
1997038 TTAAAAAAATTA
1 TTAAAAAAATTA
1997050 TTA
1 TTA
1997053 TATTTATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
TTAAAAAAATTA
Found at i:1997470 original size:19 final size:19
Alignment explanation
Indices: 1997446--1997487 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1997436 AATTTCTTTG
*
1997446 TTTTTAATATAAATTTAAT
1 TTTTTAATATAAATTGAAT
* *
1997465 TTTTTATTTTAAATTGAAT
1 TTTTTAATATAAATTGAAT
1997484 TTTT
1 TTTT
1997488 AAAATTACCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTTTAATATAAATTGAAT
Found at i:1997751 original size:2 final size:2
Alignment explanation
Indices: 1997690--1997734 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1997680 ATATTTTGTA
1997690 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
1997732 AT A
1 AT A
1997735 ATTAGGGACA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1998021 original size:21 final size:22
Alignment explanation
Indices: 1997995--1998040 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
1997985 TTGTGATATG
*
1997995 TTATC-TGCCTTTGTAGTACGT
1 TTATCATGCATTTGTAGTACGT
1998016 TTATCTATGCATTTGTAGTACGT
1 TTATC-ATGCATTTGTAGTACGT
1998039 TT
1 TT
1998041 TTCTCTGCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.23
23 17 0.77
ACGTcount: A:0.17, C:0.15, G:0.17, T:0.50
Consensus pattern (22 bp):
TTATCATGCATTTGTAGTACGT
Found at i:1998960 original size:35 final size:35
Alignment explanation
Indices: 1998921--1998987 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
1998911 TCCTCAGTTT
*
1998921 CATTCTAAACCCCAAATTTTAAAATAATTCAATTA
1 CATTCTAAACCCCAAATTCTAAAATAATTCAATTA
* *
1998956 CATTCTAAACCCTAAATTCTAAAATACTTCAA
1 CATTCTAAACCCCAAATTCTAAAATAATTCAA
1998988 AATAATATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.45, C:0.22, G:0.00, T:0.33
Consensus pattern (35 bp):
CATTCTAAACCCCAAATTCTAAAATAATTCAATTA
Found at i:1999578 original size:35 final size:34
Alignment explanation
Indices: 1999511--1999579 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 34
1999501 TATTATTTTG
* **
1999511 ATTATTTTGGAATTTGGGTTTAGAATGTAATTGA
1 ATTAGTTTGGAATTTGGGTTTAGAATAAAATTGA
1999545 ATTAGTTTGGAATTTAGGGTTTAGAATAAAATTGA
1 ATTAGTTTGGAATTT-GGGTTTAGAATAAAATTGA
1999580 GGATTGTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
34 14 0.45
35 17 0.55
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.43
Consensus pattern (34 bp):
ATTAGTTTGGAATTTGGGTTTAGAATAAAATTGA
Found at i:2000362 original size:20 final size:19
Alignment explanation
Indices: 2000321--2000368 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
2000311 AATTAGTCGC
2000321 ATTTAATTATATTATATCAT
1 ATTT-ATTATATTATATCAT
* *
2000341 ATTTATTATATTATTTTTAT
1 ATTTATTATATTA-TATCAT
2000361 ATTTATTA
1 ATTTATTA
2000369 AATACTGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTATTATATTATATCAT
Found at i:2000889 original size:23 final size:23
Alignment explanation
Indices: 2000863--2000954 Score: 68
Period size: 23 Copynumber: 4.2 Consensus size: 23
2000853 TAAGCTGCCA
* *
2000863 AAAGGCAGAGAAAAACTTGTTAC
1 AAAGGCAGAGAAAAACGTGTCAC
* * *
2000886 AAAGACAGAGATAAACGTGTCAT
1 AAAGGCAGAGAAAAACGTGTCAC
* * *
2000909 AAAGGTAGAGAAATA--TATCAC
1 AAAGGCAGAGAAAAACGTGTCAC
2000930 AAAGGCAGA-AAAATA--TGTCAC
1 AAAGGCAGAGAAAA-ACGTGTCAC
2000951 AAAG
1 AAAG
2000955 ATATAATTAT
Statistics
Matches: 54, Mismatches: 14, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
20 3 0.06
21 22 0.41
23 29 0.54
ACGTcount: A:0.51, C:0.12, G:0.21, T:0.16
Consensus pattern (23 bp):
AAAGGCAGAGAAAAACGTGTCAC
Found at i:2000943 original size:21 final size:21
Alignment explanation
Indices: 2000909--2000954 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
2000899 AACGTGTCAT
* *
2000909 AAAGGTAGAGAAATATATCAC
1 AAAGGCAGAAAAATATATCAC
*
2000930 AAAGGCAGAAAAATATGTCAC
1 AAAGGCAGAAAAATATATCAC
2000951 AAAG
1 AAAG
2000955 ATATAATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.54, C:0.11, G:0.20, T:0.15
Consensus pattern (21 bp):
AAAGGCAGAAAAATATATCAC
Found at i:2002509 original size:2 final size:2
Alignment explanation
Indices: 2002502--2002543 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
2002492 TCCAATTTTC
*
2002502 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2002544 ACCATTTATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:2007820 original size:6 final size:6
Alignment explanation
Indices: 2007789--2007834 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
2007779 TACGCAAAAA
* * *
2007789 ACATAT A-A-AT ACATAC ACACAT ACATAT ACATAT ACATAT AAATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
2007835 TTAATATGAC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
4 3 0.09
5 2 0.06
6 28 0.85
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.28
Consensus pattern (6 bp):
ACATAT
Found at i:2017942 original size:21 final size:21
Alignment explanation
Indices: 2017899--2017942 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2017889 ATATGAACTA
* *
2017899 TGGCTTTGTAAAAGTGTTGCT
1 TGGCTTTGTAAAAATGTTCCT
2017920 TGGCTTTGTAACAAAT-TTCCT
1 TGGCTTTGTAA-AAATGTTCCT
2017941 TG
1 TG
2017943 ATTTTTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.20, C:0.14, G:0.23, T:0.43
Consensus pattern (21 bp):
TGGCTTTGTAAAAATGTTCCT
Found at i:2021226 original size:20 final size:19
Alignment explanation
Indices: 2021198--2021244 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
2021188 TAATTTTATT
2021198 AATAA-AATAATAATAT-AA
1 AATAATAATAATAAT-TGAA
2021216 AACTAATAATAATAATTGAA
1 AA-TAATAATAATAATTGAA
2021236 AATAATAAT
1 AATAATAAT
2021245 TAACAAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 2 0.08
19 11 0.42
20 13 0.50
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (19 bp):
AATAATAATAATAATTGAA
Found at i:2021820 original size:139 final size:139
Alignment explanation
Indices: 2021609--2022036 Score: 491
Period size: 139 Copynumber: 3.1 Consensus size: 139
2021599 TGGAGATGAT
* ** * * * *
2021609 TTTGGAGACGACACAGTTCCTTCACACTGAGGAAAT-TAGATTGTTTGAGGATGACACTGCTCAT
1 TTTGGAGACAACACAGTTCCTTCACGTTGAGGAAGTCT-GATTGTCTGAGGATGAAACTGCTCCT
** * *
2021673 TCGTGTTGAGGAGATCTAGTCGGTGGACGACATTGTTCCTTCGTGATGAGGAAGTCTAGTCGTCT
65 TCACGTTGAGGAGATATGGTCGGTGGACGACATTGTTCCTTCGTGATGAGGAAGTCTAGTCGTCT
2021738 TTAGGGATAA
130 TTAGGGATAA
* * * * *
2021748 TTTGGAGATAACACGGTTCCTTTACGTTGAGGAAGTCTGATTGTCTGAGGATGAAATTTCTCCTT
1 TTTGGAGACAACACAGTTCCTTCACGTTGAGGAAGTCTGATTGTCTGAGGATGAAACTGCTCCTT
** * * * * * * *
2021813 TGCGTTGAGGAGATTTGGTCGATGGACGAAAATT-TTCATTCGTGATGAGGATGTCTAATCATCT
66 CACGTTGAGGAGATATGGTCGGTGGACG-ACATTGTTCCTTCGTGATGAGGAAGTCTAGTCGTCT
2021877 TTAGGGATAA
130 TTAGGGATAA
** *
2021887 TTTGGAGACAACACAGTTCCTTCGTGTTGAGGAAGTCTGATTGTCTGAGGATGACACTGCTCCTT
1 TTTGGAGACAACACAGTTCCTTCACGTTGAGGAAGTCTGATTGTCTGAGGATGAAACTGCTCCTT
* * * * ** * *
2021952 CATGTTGTGGAGATATGGTCGGTGGACAACATTGTTACTTTATGATGAGGACGTCTAGCCGTCTT
66 CACGTTGAGGAGATATGGTCGGTGGACGACATTGTTCCTTCGTGATGAGGAAGTCTAGTCGTCTT
*
2022017 TAAGGATAA
131 TAGGGATAA
2022026 TTTGGAGACAA
1 TTTGGAGACAA
2022037 TAATCTCAAG
Statistics
Matches: 239, Mismatches: 47, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
138 4 0.02
139 230 0.96
140 5 0.02
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (139 bp):
TTTGGAGACAACACAGTTCCTTCACGTTGAGGAAGTCTGATTGTCTGAGGATGAAACTGCTCCTT
CACGTTGAGGAGATATGGTCGGTGGACGACATTGTTCCTTCGTGATGAGGAAGTCTAGTCGTCTT
TAGGGATAA
Found at i:2022100 original size:37 final size:36
Alignment explanation
Indices: 2022057--2022289 Score: 138
Period size: 37 Copynumber: 6.7 Consensus size: 36
2022047 TGAGATTAAT
* *
2022057 TTTGTTTCAAGAGAAACTGTCTCAAGCAAGATGAAAA
1 TTTGTTTCAAGAGAAACTATCTCAAGCAAGA-CAAAA
* * **
2022094 TTTGTTTCGAGAGAAACAATCTC-A--AAG----GT
1 TTTGTTTCAAGAGAAACTATCTCAAGCAAGACAAAA
*
2022123 TTATGTTTCAAGAGAAACTATCTCAAGCGAGACAAAA
1 TT-TGTTTCAAGAGAAACTATCTCAAGCAAGACAAAA
* **
2022160 CTTTGTTTTAAGAGAAA-TAATCTC-A--AAG----GT
1 -TTTGTTTCAAGAGAAACT-ATCTCAAGCAAGACAAAA
* * *
2022190 TTATGTTTCAAGAGAAACTGTCTCAAACGAGACAAAA
1 TT-TGTTTCAAGAGAAACTATCTCAAGCAAGACAAAA
*
2022227 CTTTGTTTCAAGAGAAAC-AGTCTCAAGCGAGACAAAA
1 -TTTGTTTCAAGAGAAACTA-TCTCAAGCAAGACAAAA
* *
2022264 TTTGGTTTCAAAAGAAACAATCTCAA
1 TTT-GTTTCAAGAGAAACTATCTCAA
2022290 AGGTTTATGT
Statistics
Matches: 151, Mismatches: 22, Indels: 46
0.69 0.10 0.21
Matches are distributed among these distances:
29 4 0.03
30 36 0.24
31 3 0.02
33 4 0.03
34 5 0.03
36 6 0.04
37 88 0.58
38 5 0.03
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.27
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTATCTCAAGCAAGACAAAA
Found at i:2022137 original size:30 final size:30
Alignment explanation
Indices: 2022096--2022216 Score: 91
Period size: 30 Copynumber: 3.8 Consensus size: 30
2022086 GATGAAAATT
*
2022096 TGTTTCGAGAGAAACAATCTCAAAGGTTTA
1 TGTTTCAAGAGAAACAATCTCAAAGGTTTA
* **
2022126 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAACTT-
1 TGTTTCAAGAGAAACAATCTCAA---AG-----GTTTA
* *
2022163 TGTTTTAAGAGAAATAATCTCAAAGGTTTA
1 TGTTTCAAGAGAAACAATCTCAAAGGTTTA
**
2022193 TGTTTCAAGAGAAACTGTCTCAAA
1 TGTTTCAAGAGAAACAATCTCAAA
2022217 CGAGACAAAA
Statistics
Matches: 69, Mismatches: 13, Indels: 18
0.69 0.13 0.18
Matches are distributed among these distances:
29 2 0.03
30 41 0.59
33 2 0.03
34 2 0.03
37 20 0.29
38 2 0.03
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (30 bp):
TGTTTCAAGAGAAACAATCTCAAAGGTTTA
Found at i:2022167 original size:67 final size:67
Alignment explanation
Indices: 2022059--2022252 Score: 300
Period size: 67 Copynumber: 2.9 Consensus size: 67
2022049 AGATTAATTT
* * *
2022059 TGTTTCAAGAGAAACTGTCTCAAGCAAGATGAAAA-TTTGTTTCGAGAGAAACAATCTCAAAGGT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGA-CAAAACTTTGTTTCAAGAGAAACAATCTCAAAGGT
2022123 TTA
65 TTA
* * *
2022126 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAACTTTGTTTTAAGAGAAATAATCTCAAAGGTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGGTT
2022191 TA
66 TA
* *
2022193 TGTTTCAAGAGAAACTGTCTCAAACGAGACAAAACTTTGTTTCAAGAGAAACAGTCTCAA
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAA
2022253 GCGAGACAAA
Statistics
Matches: 115, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
66 4 0.03
67 111 0.97
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.28
Consensus pattern (67 bp):
TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGGTT
TA
Found at i:2022237 original size:104 final size:104
Alignment explanation
Indices: 2022126--2022356 Score: 342
Period size: 104 Copynumber: 2.2 Consensus size: 104
2022116 CAAAGGTTTA
* * *
2022126 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAACTTT-GTTTTAAGAGAAATAATCTCAAAGGT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAA-TTTGGTTTCAAAAGAAACAATCTCAAAGGT
2022190 TTATGTTTCAAGAGAAACTGTCTCAAACGAGACAAAACTT
65 TTATGTTTCAAGAGAAACTGTCTCAAACGAGACAAAACTT
2022230 TGTTTCAAGAGAAAC-AGTCTCAAGCGAGACAAAATTTGGTTTCAAAAGAAACAATCTCAAAGGT
1 TGTTTCAAGAGAAACTA-TCTCAAGCGAGACAAAATTTGGTTTCAAAAGAAACAATCTCAAAGGT
* * *
2022294 TTATGTTTCGAGAGAAATTGTCTCAAGCGAGACAAAACTT
65 TTATGTTTCAAGAGAAACTGTCTCAAACGAGACAAAACTT
**
2022334 TGTTTTGAGAGAAA-TAATCTCAA
1 TGTTTCAAGAGAAACT-ATCTCAA
2022357 AGGTTTATGT
Statistics
Matches: 115, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
103 4 0.03
104 110 0.96
105 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.28
Consensus pattern (104 bp):
TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATTTGGTTTCAAAAGAAACAATCTCAAAGGTT
TATGTTTCAAGAGAAACTGTCTCAAACGAGACAAAACTT
Found at i:2022308 original size:67 final size:66
Alignment explanation
Indices: 2022230--2022401 Score: 247
Period size: 67 Copynumber: 2.6 Consensus size: 66
2022220 GACAAAACTT
2022230 TGTTTCAAGAGAAACAGTCTCAAGCGAGACAAAATTTGGTTTCAAAAGAAACAATCTCAAAGGTT
1 TGTTTCAAGAGAAA-AGTCTCAAGCGAGACAAAATTTGGTTTCAAAAGAAACAATCTCAAAGGTT
2022295 TA
65 TA
* * ** * *
2022297 TGTTTCGAGAGAAATTGTCTCAAGCGAGACAAAACTTT-GTTTTGAGAGAAATAATCTCAAAGGT
1 TGTTTCAAGAGAAA-AGTCTCAAGCGAGACAAAA-TTTGGTTTCAAAAGAAACAATCTCAAAGGT
2022361 TTA
64 TTA
2022364 TGTTTCAAGAGAAAATGTCTCAAGCGAGACAAAATTTG
1 TGTTTCAAGAGAAAA-GTCTCAAGCGAGACAAAATTTG
2022402 TTTTTAGGAA
Statistics
Matches: 93, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
66 3 0.03
67 87 0.94
68 3 0.03
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (66 bp):
TGTTTCAAGAGAAAAGTCTCAAGCGAGACAAAATTTGGTTTCAAAAGAAACAATCTCAAAGGTTT
A
Found at i:2022347 original size:171 final size:170
Alignment explanation
Indices: 2022057--2022507 Score: 635
Period size: 171 Copynumber: 2.7 Consensus size: 170
2022047 TGAGATTAAT
* * * *
2022057 TTTGTTTCAAGAGAAACTGTCTCAAGCAAGATGAAAATTTGTTTCGAGAGAAACAATCTCAAAGG
1 TTTGTTTCAAGAGAAACAGTCTCAAGCGAGATCAAAATTTGTTTCAAGAGAAACAATCTCAAAGG
*
2022122 TTTATGTTTCAAGAGAAACTATCTCAAGCGAGACAAAACTTTGTTTTAAGAGAAATAATCTCAAA
66 TTTATGTTTCGAGAGAAACTATCTCAAGCGAGACAAAACTTTGTTTTAAGAGAAATAATCTCAAA
*
2022187 GGTTTATGTTTCAAGAGAAACTGTCTCAAACGAGACAAAA
131 GGTTTATGTTTCAAGAGAAAATGTCTCAAACGAGACAAAA
*
2022227 CTTTGTTTCAAGAGAAACAGTCTCAAGCGAGA-CAAAATTTGGTTTCAAAAGAAACAATCTCAAA
1 -TTTGTTTCAAGAGAAACAGTCTCAAGCGAGATCAAAATTT-GTTTCAAGAGAAACAATCTCAAA
* * *
2022291 GGTTTATGTTTCGAGAGAAATTGTCTCAAGCGAGACAAAACTTTGTTTTGAGAGAAATAATCTCA
64 GGTTTATGTTTCGAGAGAAACTATCTCAAGCGAGACAAAACTTTGTTTTAAGAGAAATAATCTCA
*
2022356 AAGGTTTATGTTTCAAGAGAAAATGTCTCAAGCGAGACAAAA
129 AAGGTTTATGTTTCAAGAGAAAATGTCTCAAACGAGACAAAA
** ** * * *
2022398 TTTGTTTTTAG-GAAAACTA-TCTCAAATGAGATC-AATTTTGTTTCAAGTGAAACAATTTCAAA
1 TTTGTTTCAAGAG-AAAC-AGTCTCAAGCGAGATCAAAATTTGTTTCAAGAGAAACAATCTCAAA
* *
2022460 -ATTTATGTTTCGAGGGAAAACTATCTCAAGCGAGACAAAA-TTTGTTTT
64 GGTTTATGTTTCGAGAG-AAACTATCTCAAGCGAGACAAAACTTTGTTTT
2022508 TAGGAAAACT
Statistics
Matches: 252, Mismatches: 23, Indels: 13
0.88 0.08 0.05
Matches are distributed among these distances:
168 22 0.09
169 42 0.17
170 35 0.14
171 153 0.61
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.30
Consensus pattern (170 bp):
TTTGTTTCAAGAGAAACAGTCTCAAGCGAGATCAAAATTTGTTTCAAGAGAAACAATCTCAAAGG
TTTATGTTTCGAGAGAAACTATCTCAAGCGAGACAAAACTTTGTTTTAAGAGAAATAATCTCAAA
GGTTTATGTTTCAAGAGAAAATGTCTCAAACGAGACAAAA
Found at i:2022438 original size:36 final size:36
Alignment explanation
Indices: 2022364--2022565 Score: 113
Period size: 36 Copynumber: 5.8 Consensus size: 36
2022354 CAAAGGTTTA
* ** *
2022364 TGTTTCAAGAGAAAA-TGTCTCAAGCGAGA-CAAAATT
1 TGTTTCAAG-GAAAACTATCTCAAATGAGATC-AATTT
**
2022400 TGTTTTTAGGAAAACTATCTCAAATGAGATCAATTT
1 TGTTTCAAGGAAAACTATCTCAAATGAGATCAATTT
* * *
2022436 TGTTTCAAGTG-AAACAATTTC-AA--A-AT---TTA
1 TGTTTCAAG-GAAAACTATCTCAAATGAGATCAATTT
* ** *
2022465 TGTTTCGAGGGAAAACTATCTCAAGCGAGA-CAAAATT
1 TGTTTC-AAGGAAAACTATCTCAAATGAGATC-AATTT
** *
2022502 TGTTTTTAGGAAAACTATCTCAAGTGAGATCAATTT
1 TGTTTCAAGGAAAACTATCTCAAATGAGATCAATTT
* *
2022538 T-TTTCAAGAAAAACTGTCTCAAATGAGA
1 TGTTTCAAGGAAAACTATCTCAAATGAGA
2022566 CGAAACTTTA
Statistics
Matches: 125, Mismatches: 27, Indels: 29
0.69 0.15 0.16
Matches are distributed among these distances:
29 9 0.07
30 10 0.08
31 1 0.01
32 2 0.02
33 2 0.02
34 1 0.01
35 29 0.23
36 62 0.50
37 9 0.07
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (36 bp):
TGTTTCAAGGAAAACTATCTCAAATGAGATCAATTT
Found at i:2022487 original size:102 final size:100
Alignment explanation
Indices: 2022360--2022545 Score: 318
Period size: 102 Copynumber: 1.8 Consensus size: 100
2022350 ATCTCAAAGG
*
2022360 TTTATGTTTCAAGAGAAAATGTCTCAAGCGAGACAAAATTTGTTTTTAGGAAAACTATCTCAAAT
1 TTTATGTTTCAAGAGAAAATATCTCAAGCGAGACAAAATTTGTTTTTAGGAAAACTATCTCAAAT
2022425 GAGATCAATTTTGTTTCAAGTGAAACAATTTCAAAA
66 GAGATCAATTTT-TTTCAAGTGAAACAATTTCAAAA
* * *
2022461 TTTATGTTTCGAGGGAAAACTATCTCAAGCGAGACAAAATTTGTTTTTAGGAAAACTATCTCAAG
1 TTTATGTTTCAAGAGAAAA-TATCTCAAGCGAGACAAAATTTGTTTTTAGGAAAACTATCTCAAA
2022526 TGAGATCAATTTTTTTCAAG
65 TGAGATCAATTTTTTTCAAG
2022546 AAAAACTGTC
Statistics
Matches: 80, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
101 24 0.30
102 56 0.70
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.34
Consensus pattern (100 bp):
TTTATGTTTCAAGAGAAAATATCTCAAGCGAGACAAAATTTGTTTTTAGGAAAACTATCTCAAAT
GAGATCAATTTTTTTCAAGTGAAACAATTTCAAAA
Found at i:2028917 original size:13 final size:14
Alignment explanation
Indices: 2028899--2028930 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
2028889 ATAAAATAAT
2028899 AATAATAATTAA-A
1 AATAATAATTAACA
2028912 AATAATAATTAACA
1 AATAATAATTAACA
2028926 AATAA
1 AATAA
2028931 GACCCATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (14 bp):
AATAATAATTAACA
Found at i:2029027 original size:11 final size:11
Alignment explanation
Indices: 2029011--2029036 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2029001 ATTATATTTT
2029011 AATTTTAATAA
1 AATTTTAATAA
2029022 AATTTTAATAA
1 AATTTTAATAA
2029033 AATT
1 AATT
2029037 ATATTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
AATTTTAATAA
Found at i:2032810 original size:19 final size:18
Alignment explanation
Indices: 2032788--2032837 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
2032778 AAATTGCTTA
2032788 AAATAAAATAAAAATAGCT
1 AAATAAAATAAAAATAG-T
2032807 AAATAAAA-AATAAATAGT
1 AAATAAAATAA-AAATAGT
* *
2032825 GAATAAATTAAAA
1 AAATAAAATAAAA
2032838 TAAAATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 11 0.41
19 16 0.59
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.22
Consensus pattern (18 bp):
AAATAAAATAAAAATAGT
Found at i:2034440 original size:152 final size:152
Alignment explanation
Indices: 2034154--2034465 Score: 358
Period size: 152 Copynumber: 2.1 Consensus size: 152
2034144 TTCTCTACTA
* * * * * **
2034154 GAAATGTTGGTCCCTCAAGTGAGGCGTCACTGATTTGAAGTGCTGTGAATCGAACCAAGGTTGAA
1 GAAATGTTGATCCCTCAAGTAAGGCATCACTGATTCGAAGTGCTGTGAATCGAACAAAGGTCAAA
* * * * ** *
2034219 TAAGTTCTTCTCATGATTTTTCTACTTGAAATGGTGGTTCCTGGTATGAAGCGTCGCTGATTCGA
66 CAAGTTCTTCTCATGAATTCTCTACTTGAAATGGTGGTCCCTCATATGAAGCGTCGCTGATTCAA
* *
2034284 AGTGTTGTGAATGGAGCAA-AG
131 AGTGTCGTAAATGGAGCAATAG
*** * *
2034305 GAAATGTTGATCCCTCAAGTAAGGCATTGTTGATTCGAAGTGTTGTGAATCGAGCAATAGGTCAA
1 GAAATGTTGATCCCTCAAGTAAGGCATCACTGATTCGAAGTGCTGTGAATCGAACAA-AGGTCAA
* * *
2034370 ACAAGTTCTTCTCATGAATTCTCTA-TTAGAAATGTTGGTCCCTCATGTGATGCGTCGCTGATTC
65 ACAAGTTCTTCTCATGAATTCTCTACTT-GAAATGGTGGTCCCTCATATGAAGCGTCGCTGATTC
* *
2034434 AAAGTGTCGTAAATTGAGTAATAG
129 AAAGTGTCGTAAATGGAGCAATAG
2034458 GAAATGTT
1 GAAATGTT
2034466 AACCCCTCTG
Statistics
Matches: 132, Mismatches: 26, Indels: 4
0.81 0.16 0.02
Matches are distributed among these distances:
151 49 0.37
152 73 0.55
153 10 0.08
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.32
Consensus pattern (152 bp):
GAAATGTTGATCCCTCAAGTAAGGCATCACTGATTCGAAGTGCTGTGAATCGAACAAAGGTCAAA
CAAGTTCTTCTCATGAATTCTCTACTTGAAATGGTGGTCCCTCATATGAAGCGTCGCTGATTCAA
AGTGTCGTAAATGGAGCAATAG
Found at i:2034514 original size:153 final size:152
Alignment explanation
Indices: 2034220--2034514 Score: 349
Period size: 152 Copynumber: 1.9 Consensus size: 152
2034210 AAGGTTGAAT
* * * ** *
2034220 AAGTTCTTCTCATGATTTTTCTACTTGAAATGGTGGTTCCTGGTATGAAGCGTCGCTGATTCGAA
1 AAGTTCTTCTCATGAATTCTCTACTTGAAATGGTGGTCCCTCATATGAAGCGTCGCTGATTCAAA
* * * * *
2034285 GTGTTGTGAATGGAGCAAAGGAAATGTTGATCCCTCAAGTAAGGCATTGTTGATTCGAAGTGTTG
66 GTGTCGTAAATGGAGCAAAGGAAATGTTAACCCCTCAAGTAAGGCATTGTTGATTCGAAGTATTG
*
2034350 TGAATCGAGCAATAGGTCAAAC
131 TGAATCAAGCAATAGGTCAAAC
* * *
2034372 AAGTTCTTCTCATGAATTCTCTA-TTAGAAATGTTGGTCCCTCATGTGATGCGTCGCTGATTCAA
1 AAGTTCTTCTCATGAATTCTCTACTT-GAAATGGTGGTCCCTCATATGAAGCGTCGCTGATTCAA
* * ** ** ** *
2034436 AGTGTCGTAAATTGAGTAATAGGAAATGTTAACCCCTCTGGTGGGGTGTTGTTGATTCGAATTAT
65 AGTGTCGTAAATGGAGCAA-AGGAAATGTTAACCCCTCAAGTAAGGCATTGTTGATTCGAAGTAT
2034501 TGTGAATCAAGCAA
129 TGTGAATCAAGCAA
2034515 AGGAAATGTT
Statistics
Matches: 117, Mismatches: 24, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
151 2 0.02
152 67 0.57
153 48 0.41
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.34
Consensus pattern (152 bp):
AAGTTCTTCTCATGAATTCTCTACTTGAAATGGTGGTCCCTCATATGAAGCGTCGCTGATTCAAA
GTGTCGTAAATGGAGCAAAGGAAATGTTAACCCCTCAAGTAAGGCATTGTTGATTCGAAGTATTG
TGAATCAAGCAATAGGTCAAAC
Found at i:2034637 original size:39 final size:39
Alignment explanation
Indices: 2034573--2035155 Score: 820
Period size: 39 Copynumber: 15.1 Consensus size: 39
2034563 AATCTCAAAT
2034573 GATATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGA
1 GATA-AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGA
* * * *
2034613 GATAAAATATTATGTTTTGAGTGAAACTATATCAAGCGA
1 GATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGA
* * * *
2034652 GATAAAATATTTTATTTCGAGTGAAATTATCTCAAGCGA
1 GATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGA
* *
2034691 GATAAAATCTTTTGTTTCGAGTGAAACTATTTCAAGCGA
1 GATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGA
2034730 GATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGA
1 GATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGA
* * *
2034769 GATAAAATGTTTTGTTTCGAGTGAAACTATTTCAAGCGA
1 GATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGA
* *
2034808 GATAAAATCTTTTGTTTCGAGTGAAACTATCTCAAGCAA
1 GATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGA
* * * * *
2034847 GATAAAATCTTCTATTTTGAGTGAAACTCTCTTAACCGA
1 GATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGA
2034886 GAT-AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGA
1 GATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGA
* *
2034924 GAT-AAATCTTCTGTTTTGAGTGAAACAATCTCAAGCGA
1 GATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGA
*
2034962 GAT-AAATCTTCT-TTTCGAGTG-AAGTAATCTCAAGCGA
1 GATAAAATCTTCTGTTTCGAGTGAAACT-ATCTCAAGCGA
*
2034999 GAT-AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCAA
1 GATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGA
* * * *
2035037 GAT-AAATATTATGTTTCGAGTGAAACAATCTCAAGTGA
1 GATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGA
* * *
2035075 GATAAAATCTTGTATTTTGAGTGAAACTATCTCAAGCGA
1 GATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGA
2035114 GATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGA
1 GATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGA
2035153 GAT
1 GAT
2035156 GAATCTTGTT
Statistics
Matches: 485, Mismatches: 54, Indels: 9
0.89 0.10 0.02
Matches are distributed among these distances:
36 2 0.00
37 31 0.06
38 133 0.27
39 315 0.65
40 4 0.01
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (39 bp):
GATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGA
Found at i:2036808 original size:116 final size:116
Alignment explanation
Indices: 2036604--2036840 Score: 474
Period size: 116 Copynumber: 2.0 Consensus size: 116
2036594 TTATTGTATA
2036604 ATTTATAGTAATGATAATAATTATTAACCTTTTGAGTATTTAGCTATAGAATTTCTTAAGCTCAT
1 ATTTATAGTAATGATAATAATTATTAACCTTTTGAGTATTTAGCTATAGAATTTCTTAAGCTCAT
2036669 CGAGAAGAACCTATTATAGTCTAGGTGTCTTTGATTGTAAGGAAATCTGAC
66 CGAGAAGAACCTATTATAGTCTAGGTGTCTTTGATTGTAAGGAAATCTGAC
2036720 ATTTATAGTAATGATAATAATTATTAACCTTTTGAGTATTTAGCTATAGAATTTCTTAAGCTCAT
1 ATTTATAGTAATGATAATAATTATTAACCTTTTGAGTATTTAGCTATAGAATTTCTTAAGCTCAT
2036785 CGAGAAGAACCTATTATAGTCTAGGTGTCTTTGATTGTAAGGAAATCTGAC
66 CGAGAAGAACCTATTATAGTCTAGGTGTCTTTGATTGTAAGGAAATCTGAC
2036836 ATTTA
1 ATTTA
2036841 GAGTTTAGTT
Statistics
Matches: 121, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
116 121 1.00
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (116 bp):
ATTTATAGTAATGATAATAATTATTAACCTTTTGAGTATTTAGCTATAGAATTTCTTAAGCTCAT
CGAGAAGAACCTATTATAGTCTAGGTGTCTTTGATTGTAAGGAAATCTGAC
Found at i:2041974 original size:24 final size:24
Alignment explanation
Indices: 2041918--2041974 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
2041908 TTGATTTCTA
* *
2041918 TTATGATACTTGACATGGTTTATG
1 TTATGATATTTGACATGGATTATG
2041942 TTATGATATTTGATC-TGGATTATG
1 TTATGATATTTGA-CATGGATTATG
2041966 TTATGATAT
1 TTATGATAT
2041975 CTAACCTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 29 0.97
25 1 0.03
ACGTcount: A:0.26, C:0.05, G:0.19, T:0.49
Consensus pattern (24 bp):
TTATGATATTTGACATGGATTATG
Found at i:2041987 original size:24 final size:24
Alignment explanation
Indices: 2041937--2041996 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
2041927 TTGACATGGT
* * * *
2041937 TTATGTTATGATATTTGATCTGGA
1 TTATGTTATGATATCTAACCTGAA
2041961 TTATGTTATGATATCTAACCTGAA
1 TTATGTTATGATATCTAACCTGAA
*
2041985 TTATGTTTTGAT
1 TTATGTTATGAT
2041997 TTTTTATAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.27, C:0.07, G:0.17, T:0.50
Consensus pattern (24 bp):
TTATGTTATGATATCTAACCTGAA
Found at i:2042279 original size:155 final size:155
Alignment explanation
Indices: 2042021--2042329 Score: 501
Period size: 155 Copynumber: 2.0 Consensus size: 155
2042011 TTACGAACGA
*
2042021 AAATATTTTATTTGGGGGTATTGGTGGAGGAAGAATACTTGCAGGCTCCTTAGCTTTGTGCTCAG
1 AAATATTTTATTTGGGGGTATTGGTGGAGGAAGAATACTTGCAGGCTCCTCAGCTTTGTGCTCAG
* *
2042086 GGCCTTACTCGATGTGACGGTGGGTGTATAGTTCTGGGGAACCTACACATAATGATGTGTTTGGT
66 GGCCTTACTCGATGTGACGGTGGGTGTATAGTTCTGGGGAACCTACACATAATGATGTGTTGGGC
2042151 TGGAGGGATTACTATGGTTTTTGAT
131 TGGAGGGATTACTATGGTTTTTGAT
* * * * * *
2042176 AAATGTTTTATTTGGGGGTATTGTTGGAGGAAGTATATTTGTAGGCTCCTCATCTTTGTGCTCAG
1 AAATATTTTATTTGGGGGTATTGGTGGAGGAAGAATACTTGCAGGCTCCTCAGCTTTGTGCTCAG
* * *
2042241 GGCCTTACTCGATGTGACGGTGGGTGTATGGTTTTGGGGAACCTACACATTATGATGTGTTGGGC
66 GGCCTTACTCGATGTGACGGTGGGTGTATAGTTCTGGGGAACCTACACATAATGATGTGTTGGGC
*
2042306 TGGAGGGATTATTATGGTTTTTGA
131 TGGAGGGATTACTATGGTTTTTGA
2042330 ATTTAAAAAA
Statistics
Matches: 141, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
155 141 1.00
ACGTcount: A:0.20, C:0.12, G:0.31, T:0.37
Consensus pattern (155 bp):
AAATATTTTATTTGGGGGTATTGGTGGAGGAAGAATACTTGCAGGCTCCTCAGCTTTGTGCTCAG
GGCCTTACTCGATGTGACGGTGGGTGTATAGTTCTGGGGAACCTACACATAATGATGTGTTGGGC
TGGAGGGATTACTATGGTTTTTGAT
Found at i:2044170 original size:15 final size:14
Alignment explanation
Indices: 2044144--2044200 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 14
2044134 GACCCTCCTG
*
2044144 CCCGATTGAGTCAA
1 CCCGACTGAGTCAA
2044158 CCCGTACTGAGTCAA
1 CCCG-ACTGAGTCAA
* *
2044173 CTCGGCTGAGTCAA
1 CCCGACTGAGTCAA
* *
2044187 CTC-ACTGGGTCAA
1 CCCGACTGAGTCAA
2044200 C
1 C
2044201 TCGTTGACCG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
13 9 0.24
14 16 0.43
15 12 0.32
ACGTcount: A:0.25, C:0.32, G:0.23, T:0.21
Consensus pattern (14 bp):
CCCGACTGAGTCAA
Found at i:2044200 original size:13 final size:14
Alignment explanation
Indices: 2044150--2044203 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
2044140 CCTGCCCGAT
*
2044150 TGAGTCAACCCGTAC
1 TGAGTCAACTCG-AC
*
2044165 TGAGTCAACTCGGC
1 TGAGTCAACTCGAC
2044179 TGAGTCAACTC-AC
1 TGAGTCAACTCGAC
*
2044192 TGGGTCAACTCG
1 TGAGTCAACTCG
2044204 TTGACCGTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
13 11 0.32
14 12 0.35
15 11 0.32
ACGTcount: A:0.24, C:0.30, G:0.24, T:0.22
Consensus pattern (14 bp):
TGAGTCAACTCGAC
Found at i:2044237 original size:30 final size:30
Alignment explanation
Indices: 2044190--2044251 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
2044180 GAGTCAACTC
*
2044190 ACTGGGTCAACTCGTTGACCGTTGACTTTG
1 ACTGAGTCAACTCGTTGACCGTTGACTTTG
*
2044220 ACTGAGTCAAC-CAGTTGATCGTTGACTTTG
1 ACTGAGTCAACTC-GTTGACCGTTGACTTTG
2044250 AC
1 AC
2044252 CAAAAAGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 1 0.03
30 28 0.97
ACGTcount: A:0.21, C:0.23, G:0.24, T:0.32
Consensus pattern (30 bp):
ACTGAGTCAACTCGTTGACCGTTGACTTTG
Found at i:2045194 original size:18 final size:18
Alignment explanation
Indices: 2045168--2045205 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2045158 TGGAAAGCAC
*
2045168 TGAAGTAAATGATAAATT
1 TGAAGTAAATAATAAATT
*
2045186 TGAATTAAATAATAAATT
1 TGAAGTAAATAATAAATT
2045204 TG
1 TG
2045206 GATGGGAGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (18 bp):
TGAAGTAAATAATAAATT
Found at i:2045408 original size:24 final size:24
Alignment explanation
Indices: 2045380--2045428 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
2045370 TAGCCTAGAC
*
2045380 TAAGTAAATGTCGTGGATTAAATA
1 TAAGTAAATGACGTGGATTAAATA
2045404 TAAGTAAATGACGTGGATTAAATA
1 TAAGTAAATGACGTGGATTAAATA
2045428 T
1 T
2045429 TGGATTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.20, T:0.33
Consensus pattern (24 bp):
TAAGTAAATGACGTGGATTAAATA
Found at i:2048991 original size:22 final size:22
Alignment explanation
Indices: 2048966--2049049 Score: 66
Period size: 24 Copynumber: 3.8 Consensus size: 22
2048956 CAGAACCCGT
*
2048966 AGGGGTATCGATTCCC-TCAAG
1 AGGGGAATCGATTCCCTTCAAG
* *
2048987 -GAGGGAATCGGTTCCCATTCAAA
1 AG-GGGAATCGATTCCC-TTCAAG
*
2049010 AGGGGGAATCGGTTCCTCTTCAAG
1 A-GGGGAATCGATTCC-CTTCAAG
*
2049034 -GGGGTATCGATTCCCT
1 AGGGGAATCGATTCCCT
2049050 CTGCACTAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
20 1 0.02
21 14 0.27
22 12 0.24
23 4 0.08
24 18 0.35
25 2 0.04
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.25
Consensus pattern (22 bp):
AGGGGAATCGATTCCCTTCAAG
Found at i:2054983 original size:51 final size:51
Alignment explanation
Indices: 2054928--2055099 Score: 233
Period size: 51 Copynumber: 3.4 Consensus size: 51
2054918 CTTAAAGGAC
*
2054928 TAAATTGCATAAAATAAAATAACAGTAGCTAAATCAGAAATAAACAATAAA
1 TAAATTGCATAAAATAAAATAACAGTAGCTAAATCAGAAATAAACAATGAA
* * * *
2054979 TAAATTGCATAAAATAAAATAACAGCAACTAAAT-A-AAA-AAATAGTGAA
1 TAAATTGCATAAAATAAAATAACAGTAGCTAAATCAGAAATAAACAATGAA
* *
2055027 TAAATTGCATAAAATAAAATAACAGTAGCTAAATCAGAAATAAACATTGAC
1 TAAATTGCATAAAATAAAATAACAGTAGCTAAATCAGAAATAAACAATGAA
**
2055078 TAAATTAAAATAAAATAAAATA
1 TAAATT-GCATAAAATAAAATA
2055100 GAATGATAAA
Statistics
Matches: 105, Mismatches: 12, Indels: 7
0.85 0.10 0.06
Matches are distributed among these distances:
48 39 0.37
49 4 0.04
50 4 0.04
51 45 0.43
52 13 0.12
ACGTcount: A:0.61, C:0.09, G:0.08, T:0.23
Consensus pattern (51 bp):
TAAATTGCATAAAATAAAATAACAGTAGCTAAATCAGAAATAAACAATGAA
Found at i:2056825 original size:21 final size:21
Alignment explanation
Indices: 2056776--2056839 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
2056766 TATATGAAAT
* *
2056776 TTGTCCTGAAGGACCTGTGAA
1 TTGTCCCGAAGGACCTATGAA
* *
2056797 TATGTCCCGAATGACCTATGAG
1 T-TGTCCCGAAGGACCTATGAA
2056819 TTGTCCCGAAGGACCTATGAA
1 TTGTCCCGAAGGACCTATGAA
2056840 ACCCTCGACT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
21 19 0.53
22 17 0.47
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.27
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAA
Found at i:2060103 original size:25 final size:25
Alignment explanation
Indices: 2060074--2060130 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
2060064 ATCTATTTTG
*
2060074 TCATCTTTGTTGAGATTACGATTTA
1 TCATCTCTGTTGAGATTACGATTTA
2060099 TCATCTCTGTTGAGATTACGATTTA
1 TCATCTCTGTTGAGATTACGATTTA
2060124 TCATCTC
1 TCATCTC
2060131 CTTGTTCTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.46
Consensus pattern (25 bp):
TCATCTCTGTTGAGATTACGATTTA
Found at i:2060326 original size:23 final size:23
Alignment explanation
Indices: 2060283--2060327 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2060273 CACAATTAAT
*
2060283 ATAAAATTAAAATTTTAAAAAAA
1 ATAAAATTAAAATTATAAAAAAA
*
2060306 ATAAAATTAATATTAATAAAAA
1 ATAAAATTAAAATT-ATAAAAA
2060328 CTACTTGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (23 bp):
ATAAAATTAAAATTATAAAAAAA
Found at i:2062636 original size:84 final size:84
Alignment explanation
Indices: 2062467--2062691 Score: 233
Period size: 84 Copynumber: 2.7 Consensus size: 84
2062457 TGTAATGACG
* * * **
2062467 TTTTTC-AACAAACGCCACAACATAGTAGTACTTTAGCGGCGTTTTTATACAAACT-CTGCAATA
1 TTTTTCTAACAAACGCCGCAACATATTAGTACTTTAGCGGCGTTTTTATA-AAAATGCCACAATA
*
2062530 AGTCCATCTATAGTGTTATT
65 AGTCCATCTATAGTGTGATT
* * *
2062550 TTTTTCTAACAAACGCCGCAAAAGATTTGTACTTTAGCGGCGTTTTTATAAAAATGCCACAATAG
1 TTTTTCTAACAAACGCCGCAACATATTAGTACTTTAGCGGCGTTTTTATAAAAATGCCACAATA-
* *
2062615 AGTTC-TCCTATAGTG-GCTT
65 AGTCCAT-CTATAGTGTGATT
* * * * * * *
2062634 TTTTTCTAATAAGCGCTGTAACATATTAGAACTTTAGCGGCGTTTTTACACAAATGCC
1 TTTTTCTAACAAACGCCGCAACATATTAGTACTTTAGCGGCGTTTTTATAAAAATGCC
2062692 GCAAAAAATA
Statistics
Matches: 117, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
83 10 0.09
84 95 0.81
85 12 0.10
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (84 bp):
TTTTTCTAACAAACGCCGCAACATATTAGTACTTTAGCGGCGTTTTTATAAAAATGCCACAATAA
GTCCATCTATAGTGTGATT
Found at i:2066231 original size:85 final size:85
Alignment explanation
Indices: 2066058--2066384 Score: 362
Period size: 85 Copynumber: 3.8 Consensus size: 85
2066048 ATTAGCGGCA
* * * * *
2066058 TTTGTATCCAAAAACGCCACTATAG-ATTTAACCTTTTGCGGCGTTT-TTGGA-AAAATGCCGCT
1 TTTGT-TCCAAAAACGCCGCTATAGAACTCAACCTTTTGCGGCGTTTGTT-CATAAAACGCCGCT
*
2066120 ATAGATGT-AGACCTTTTGCGACG
64 ATAGATCTCA-A-CTTTTGCGACG
* * *
2066143 TTTGTTCCAAAAACGCCGCTATAGAACTCAACCTTTTGTGGCGTTTGTTTATAAAATGCCGCTAT
1 TTTGTTCCAAAAACGCCGCTATAGAACTCAACCTTTTGCGGCGTTTGTTCATAAAACGCCGCTAT
2066208 AGATCTCAACGTTTT-CGGA-G
66 AGATCTCAAC-TTTTGC-GACG
* * * * *
2066228 TTTGCTCCAAAAATGCCGCTATAAAACTCAACCTTTTGCGGTGTTTGTTCATAAAACACCGCTAT
1 TTTGTTCCAAAAACGCCGCTATAGAACTCAACCTTTTGCGGCGTTTGTTCATAAAACGCCGCTAT
*
2066293 AGATCTCGACTTTTTGCGACG
66 AGATCTCAAC-TTTTGCGACG
* * * *
2066314 TTTGTTCTAAAAACGCCGCTATAGATA-TCACCCTTTTGCGACGTTTGTTCAAAAAACGCCGCTA
1 TTTGTTCCAAAAACGCCGCTATAGA-ACTCAACCTTTTGCGGCGTTTGTTCATAAAACGCCGCTA
2066378 TAGATCT
65 TAGATCT
2066385 TGACCTATGG
Statistics
Matches: 208, Mismatches: 25, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
84 18 0.09
85 99 0.48
86 89 0.43
87 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (85 bp):
TTTGTTCCAAAAACGCCGCTATAGAACTCAACCTTTTGCGGCGTTTGTTCATAAAACGCCGCTAT
AGATCTCAACTTTTGCGACG
Found at i:2066290 original size:128 final size:129
Alignment explanation
Indices: 2066058--2066379 Score: 325
Period size: 128 Copynumber: 2.5 Consensus size: 129
2066048 ATTAGCGGCA
* * * * * **
2066058 TTTGTATCCAAAAACGCCACTATAGAT-TTAACCTTTTGCGGCGTTT-TTGGAAAAATGCCGCTA
1 TTTGT-TCTAAAAACGCCGCTATAGATATCAACCTTTTGCGACGTTTGCTCAAAAAATGCCGCTA
* ** * * *
2066121 TAGATGTAGACCTTTTGCGACGTTTGTTCCAAAAACGCCGCTATAGAACTCAACCTTTTGTGGCG
65 TAAAACTAGACCTTTTGCGACGTTTGTTCCAAAAACACCGCTATAGAACTCAACCTTTTGCGACG
* * * *
2066186 TTTGTT-TATAAAATGCCGCTATAGATCTCAACGTTTT-CGGA-GTTTGCTCCAAAAATGCCGCT
1 TTTGTTCTA-AAAACGCCGCTATAGATATCAACCTTTTGC-GACGTTTGCTCAAAAAATGCCGCT
** * * *
2066248 ATAAAACTCA-ACCTTTTGCGGTGTTTGTT-CATAAAACACCGCTATAGATCTCGACTTTTTGCG
64 ATAAAACT-AGACCTTTTGCGACGTTTGTTCCA-AAAACACCGCTATAGAACTCAACCTTTTGCG
2066311 ACG
127 ACG
* * *
2066314 TTTGTTCTAAAAACGCCGCTATAGATATCACCCTTTTGCGACGTTTGTTCAAAAAACGCCGCTAT
1 TTTGTTCTAAAAACGCCGCTATAGATATCAACCTTTTGCGACGTTTGCTCAAAAAATGCCGCTAT
2066379 A
66 A
2066380 GATCTTGACC
Statistics
Matches: 158, Mismatches: 27, Indels: 17
0.78 0.13 0.08
Matches are distributed among these distances:
126 1 0.01
127 23 0.15
128 109 0.69
129 25 0.16
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (129 bp):
TTTGTTCTAAAAACGCCGCTATAGATATCAACCTTTTGCGACGTTTGCTCAAAAAATGCCGCTAT
AAAACTAGACCTTTTGCGACGTTTGTTCCAAAAACACCGCTATAGAACTCAACCTTTTGCGACG
Found at i:2066402 original size:43 final size:43
Alignment explanation
Indices: 2066052--2066402 Score: 332
Period size: 43 Copynumber: 8.2 Consensus size: 43
2066042 TAGGTAATTA
* * * *
2066052 GCGGCATTTGTATCCAAAAACGCCACTATAGAT-TTAACCTTTT
1 GCGGCGTTTGT-TCAAAAAACGCCGCTATAGATCTCAACCTTTT
** * *
2066095 GCGGCGTTT-TTGGAAAAATGCCGCTATAGATGT-AGACCTTTT
1 GCGGCGTTTGTTCAAAAAACGCCGCTATAGATCTCA-ACCTTTT
* * *
2066137 GCGACGTTTGTTCCAAAAACGCCGCTATAGAACTCAACCTTTT
1 GCGGCGTTTGTTCAAAAAACGCCGCTATAGATCTCAACCTTTT
* * * * *
2066180 GTGGCGTTTGTTTATAAAATGCCGCTATAGATCTCAACGTTTT
1 GCGGCGTTTGTTCAAAAAACGCCGCTATAGATCTCAACCTTTT
* * * * * *
2066223 -CGGAGTTTGCTCCAAAAATGCCGCTATAAAACTCAACCTTTT
1 GCGGCGTTTGTTCAAAAAACGCCGCTATAGATCTCAACCTTTT
* * * * *
2066265 GCGGTGTTTGTTCATAAAACACCGCTATAGATCTCGACTTTTT
1 GCGGCGTTTGTTCAAAAAACGCCGCTATAGATCTCAACCTTTT
* * * *
2066308 GCGACGTTTGTTCTAAAAACGCCGCTATAGATATCACCCTTTT
1 GCGGCGTTTGTTCAAAAAACGCCGCTATAGATCTCAACCTTTT
* ** * *
2066351 GCGACGTTTGTTCAAAAAACGCCGCTATAGATCTTGACCTATG
1 GCGGCGTTTGTTCAAAAAACGCCGCTATAGATCTCAACCTTTT
2066394 GCGGCGTTT
1 GCGGCGTTT
2066403 TTCCAATCGC
Statistics
Matches: 248, Mismatches: 55, Indels: 10
0.79 0.18 0.03
Matches are distributed among these distances:
41 18 0.07
42 50 0.20
43 179 0.72
44 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (43 bp):
GCGGCGTTTGTTCAAAAAACGCCGCTATAGATCTCAACCTTTT
Found at i:2073315 original size:21 final size:21
Alignment explanation
Indices: 2073290--2073352 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
2073280 TCATAATAAT
2073290 ATATAGTGCATAAATGAGTAA
1 ATATAGTGCATAAATGAGTAA
* *
2073311 ATATA-AG-AT-AA--AGTAT
1 ATATAGTGCATAAATGAGTAA
2073327 ATATAGTGCATAAATGAGTAA
1 ATATAGTGCATAAATGAGTAA
2073348 ATATA
1 ATATA
2073353 AGATAAAGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
16 9 0.27
17 1 0.03
18 4 0.12
19 4 0.12
20 1 0.03
21 14 0.42
ACGTcount: A:0.51, C:0.03, G:0.16, T:0.30
Consensus pattern (21 bp):
ATATAGTGCATAAATGAGTAA
Found at i:2073331 original size:37 final size:37
Alignment explanation
Indices: 2073288--2073362 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
2073278 GCTCATAATA
2073288 ATATATAGTGCATAAATGAGTAAATATAAGATAAAGT
1 ATATATAGTGCATAAATGAGTAAATATAAGATAAAGT
2073325 ATATATAGTGCATAAATGAGTAAATATAAGATAAAGT
1 ATATATAGTGCATAAATGAGTAAATATAAGATAAAGT
2073362 A
1 A
2073363 AGGTAGAACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.52, C:0.03, G:0.16, T:0.29
Consensus pattern (37 bp):
ATATATAGTGCATAAATGAGTAAATATAAGATAAAGT
Found at i:2077757 original size:20 final size:20
Alignment explanation
Indices: 2077734--2077814 Score: 90
Period size: 20 Copynumber: 4.0 Consensus size: 20
2077724 CACTTGGTAG
* *
2077734 CGATAATGTTCATCAAGTAT
1 CGATATTGTTCATCTAGTAT
*
2077754 CGATATTGTTCTTGCTTAGTAT
1 CGATATTGTTCAT-C-TAGTAT
* *
2077776 CGATATTGATCATTTAGTAT
1 CGATATTGTTCATCTAGTAT
*
2077796 CGATATTGTTCATCCAGTA
1 CGATATTGTTCATCTAGTA
2077815 CTGATACTAC
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
20 33 0.66
21 1 0.02
22 16 0.32
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (20 bp):
CGATATTGTTCATCTAGTAT
Found at i:2082313 original size:2 final size:2
Alignment explanation
Indices: 2082306--2082342 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2082296 TGTATGTAAG
2082306 TA TA TA TA 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 TA TA TA TA T
2082343 TCATTTGCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2084100 original size:16 final size:17
Alignment explanation
Indices: 2084079--2084111 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2084069 TCTCAAAATT
2084079 AAAGCACGT-CGGGTAG
1 AAAGCACGTCCGGGTAG
*
2084095 AAAGCATGTCCGGGTAG
1 AAAGCACGTCCGGGTAG
2084112 GATTTTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.30, C:0.18, G:0.36, T:0.15
Consensus pattern (17 bp):
AAAGCACGTCCGGGTAG
Found at i:2084954 original size:25 final size:25
Alignment explanation
Indices: 2084916--2084969 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
2084906 AAGTTAATCG
* *
2084916 TTGACCGACTGTTGACCATTCACCA
1 TTGACCGACCGTTGACCATTCACAA
* *
2084941 TTGACTGACCGTTGACCGTTCACAA
1 TTGACCGACCGTTGACCATTCACAA
2084966 TTGA
1 TTGA
2084970 TCGTTCACCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.30
Consensus pattern (25 bp):
TTGACCGACCGTTGACCATTCACAA
Found at i:2084974 original size:14 final size:14
Alignment explanation
Indices: 2084952--2084986 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2084942 TGACTGACCG
2084952 TTGACCGTTCACAA
1 TTGACCGTTCACAA
* *
2084966 TTGATCGTTCACCA
1 TTGACCGTTCACAA
2084980 TTGACCG
1 TTGACCG
2084987 ACCGTTGACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.31
Consensus pattern (14 bp):
TTGACCGTTCACAA
Found at i:2085819 original size:39 final size:39
Alignment explanation
Indices: 2085776--2085973 Score: 177
Period size: 39 Copynumber: 5.1 Consensus size: 39
2085766 GACCTTACCG
* *
2085776 CTTTCTGCAGGCTCCTCGGCTTTGTACTCAGGATAAGTC
1 CTTTCTGCAGGCTCCTCTGCTTTGTGCTCAGGATAAGTC
* * * *
2085815 CTTTCCGTAGGCTCATC-GACTTTGTACTCAAGG-TAAGTC
1 CTTTCTGCAGGCTCCTCTG-CTTTGTGCTC-AGGATAAGTC
* * * *
2085854 CTTACTGCAAGCTCCTCTGATTTGTGCTCAGGGTAAGTC
1 CTTTCTGCAGGCTCCTCTGCTTTGTGCTCAGGATAAGTC
* * * * *
2085893 CTTACTGTAGGCTCCTCTACTTTGTGCACAGGATAAG-A
1 CTTTCTGCAGGCTCCTCTGCTTTGTGCTCAGGATAAGTC
** * *
2085931 CTTTACTGCATTCTCCTCTGCTTTGTGCACAGGGTAAGTC
1 CTTT-CTGCAGGCTCCTCTGCTTTGTGCTCAGGATAAGTC
2085971 CTT
1 CTT
2085974 ACTGGGTGTA
Statistics
Matches: 129, Mismatches: 24, Indels: 11
0.79 0.15 0.07
Matches are distributed among these distances:
38 7 0.05
39 115 0.89
40 7 0.05
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.34
Consensus pattern (39 bp):
CTTTCTGCAGGCTCCTCTGCTTTGTGCTCAGGATAAGTC
Found at i:2085915 original size:78 final size:78
Alignment explanation
Indices: 2085780--2085977 Score: 236
Period size: 78 Copynumber: 2.5 Consensus size: 78
2085770 TTACCGCTTT
* * * * * * *
2085780 CTGCAGGCTCCTCGGCTTTGTACTCAGGATAAGTCCTTTCCGTAGGCTCATCGACTTTGTACTCA
1 CTGCAAGCTCCTCTGCTTTGTGCTCAGGGTAAGTCCTTACTGTAGGCTCATCGACTTTGTACAC-
*
2085845 AGG-TAAGTCCTTA
65 AGGATAAGACCTTA
* * * *
2085858 CTGCAAGCTCCTCTGATTTGTGCTCAGGGTAAGTCCTTACTGTAGGCTCCTCTACTTTGTGCACA
1 CTGCAAGCTCCTCTGCTTTGTGCTCAGGGTAAGTCCTTACTGTAGGCTCATCGACTTTGTACACA
*
2085923 GGATAAGACTTTA
66 GGATAAGACCTTA
** *
2085936 CTGCATTCTCCTCTGCTTTGTGCACAGGGTAAGTCCTTACTG
1 CTGCAAGCTCCTCTGCTTTGTGCTCAGGGTAAGTCCTTACTG
2085978 GGTGTACAAG
Statistics
Matches: 102, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
77 3 0.03
78 99 0.97
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.33
Consensus pattern (78 bp):
CTGCAAGCTCCTCTGCTTTGTGCTCAGGGTAAGTCCTTACTGTAGGCTCATCGACTTTGTACACA
GGATAAGACCTTA
Found at i:2091584 original size:39 final size:39
Alignment explanation
Indices: 2091530--2091635 Score: 167
Period size: 39 Copynumber: 2.7 Consensus size: 39
2091520 AAGCTCATTG
* **
2091530 GCTTTGTGCTCAGGGTAAGTCCTTACTGCAGGCTTTTAT
1 GCTTTGTGCTCAGGGTAAGTCCTTACTGCAGGATACTAT
*
2091569 GCTTTGTGCTCAGGGTAAGTCCTTACTGCAGGATACTCT
1 GCTTTGTGCTCAGGGTAAGTCCTTACTGCAGGATACTAT
*
2091608 GCTTTGTGCACAGGGTAAGTCCTTACTG
1 GCTTTGTGCTCAGGGTAAGTCCTTACTG
2091636 GGTGTATGGT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 62 1.00
ACGTcount: A:0.17, C:0.22, G:0.26, T:0.35
Consensus pattern (39 bp):
GCTTTGTGCTCAGGGTAAGTCCTTACTGCAGGATACTAT
Found at i:2095328 original size:10 final size:10
Alignment explanation
Indices: 2095309--2095339 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2095299 TCAACTTTAC
*
2095309 ATTTTTATTT
1 ATTTTAATTT
2095319 ATTTTAATTT
1 ATTTTAATTT
2095329 ATTTTAATTT
1 ATTTTAATTT
2095339 A
1 A
2095340 GTCCTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
ATTTTAATTT
Found at i:2101122 original size:31 final size:31
Alignment explanation
Indices: 2101041--2101115 Score: 132
Period size: 31 Copynumber: 2.4 Consensus size: 31
2101031 TTCATTAATT
2101041 TAACCCTCGAAGTTAATTAAGAGCATCATCC
1 TAACCCTCGAAGTTAATTAAGAGCATCATCC
*
2101072 TAACCTTCGAAGTTAATTAAGAGCATCATCC
1 TAACCCTCGAAGTTAATTAAGAGCATCATCC
*
2101103 TAGCCCTCGAAGT
1 TAACCCTCGAAGT
2101116 CTATTAACCG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (31 bp):
TAACCCTCGAAGTTAATTAAGAGCATCATCC
Found at i:2109342 original size:21 final size:21
Alignment explanation
Indices: 2109318--2109359 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2109308 ATTTGAGGGT
2109318 TATATGAGGTCCTTCGGGACA
1 TATATGAGGTCCTTCGGGACA
2109339 TATATGAGGTCCTTCGGGACA
1 TATATGAGGTCCTTCGGGACA
2109360 ATTTTATATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (21 bp):
TATATGAGGTCCTTCGGGACA
Found at i:2110034 original size:90 final size:89
Alignment explanation
Indices: 2109875--2110051 Score: 291
Period size: 90 Copynumber: 2.0 Consensus size: 89
2109865 CCTAACACAC
*
2109875 CCTTTTATAGCCAAGTTAACCTAATCATATTAGGGTTTTATTATTTCAAATTATTTAAATCTATA
1 CCTTTTATAGCCAAGTTAACCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
* *
2109940 TTTAATTAATTAGAATTTAATAAT
66 TTTAATTAATTAAAATTAAATAAT
* * *
2109964 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTTAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTAACCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTAT
2110029 ATTTAATTAATTAAAATTAAATA
65 ATTTAATTAATTAAAATTAAATA
2110052 CTCGGGATTA
Statistics
Matches: 81, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 33 0.41
90 48 0.59
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTAACCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
TTTAATTAATTAAAATTAAATAAT
Found at i:2116282 original size:8 final size:8
Alignment explanation
Indices: 2116269--2116302 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
2116259 TCAATTGAAA
2116269 AACATATT
1 AACATATT
2116277 AACATATT
1 AACATATT
*
2116285 AACAAATT
1 AACATATT
2116293 AACATATT
1 AACATATT
2116301 AA
1 AA
2116303 TCTTTGCGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (8 bp):
AACATATT
Found at i:2121914 original size:2 final size:2
Alignment explanation
Indices: 2121907--2122013 Score: 214
Period size: 2 Copynumber: 53.5 Consensus size: 2
2121897 TTATTTTACG
2121907 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
2121949 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
2121991 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
2122014 TAAAGATGTT
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 105 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2127856 original size:24 final size:23
Alignment explanation
Indices: 2127819--2127874 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 23
2127809 TCGAAATTGT
* * *
2127819 CACATATAATTGTACCGAAGTGC
1 CACATAGAATTGTACCAAAGTGA
*
2127842 CGCATAGAATATGTACCAAAGTGA
1 CACATAGAAT-TGTACCAAAGTGA
2127866 CACATAGAA
1 CACATAGAA
2127875 ACGTCCCTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 8 0.30
24 19 0.70
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (23 bp):
CACATAGAATTGTACCAAAGTGA
Found at i:2127909 original size:23 final size:23
Alignment explanation
Indices: 2127866--2127959 Score: 75
Period size: 23 Copynumber: 4.0 Consensus size: 23
2127856 ACCAAAGTGA
* *
2127866 CACATAGAAACGT-CCCTAAGGAC
1 CACATAGAAA-TTACCCGAAGGAC
2127889 CACATAGAAATTACCCGAAGGAC
1 CACATAGAAATTACCCGAAGGAC
* * * **
2127912 CGCGTAGAATTTATCTTGAAGGAC
1 CACATAGAAATTA-CCCGAAGGAC
*
2127936 CACATAG-AATTGTCCCGAAGGAC
1 CACATAGAAATT-ACCCGAAGGAC
2127959 C
1 C
2127960 GCGTAGAACC
Statistics
Matches: 55, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
22 1 0.02
23 41 0.75
24 13 0.24
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.18
Consensus pattern (23 bp):
CACATAGAAATTACCCGAAGGAC
Found at i:2127966 original size:23 final size:24
Alignment explanation
Indices: 2127878--2127967 Score: 85
Period size: 23 Copynumber: 3.8 Consensus size: 24
2127868 CATAGAAACG
* * * *
2127878 TCCCTAAGGACCACATAGAAATTA
1 TCCCGAAGGACCGCGTAGAATTTA
2127902 -CCCGAAGGACCGCGTAGAATTTA
1 TCCCGAAGGACCGCGTAGAATTTA
** * * *
2127925 TCTTGAAGGACCACATAGAA-TTG
1 TCCCGAAGGACCGCGTAGAATTTA
2127948 TCCCGAAGGACCGCGTAGAA
1 TCCCGAAGGACCGCGTAGAA
2127968 CCCTCGACTC
Statistics
Matches: 52, Mismatches: 13, Indels: 3
0.76 0.19 0.04
Matches are distributed among these distances:
23 37 0.71
24 15 0.29
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.19
Consensus pattern (24 bp):
TCCCGAAGGACCGCGTAGAATTTA
Found at i:2131833 original size:27 final size:27
Alignment explanation
Indices: 2131795--2131849 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
2131785 TTTCTAAAGA
2131795 ATCTTGCGTTTGTGTCCCAACATATTT
1 ATCTTGCGTTTGTGTCCCAACATATTT
2131822 ATCTTGCGTTTGTGTCCCAACATATTT
1 ATCTTGCGTTTGTGTCCCAACATATTT
2131849 A
1 A
2131850 ACCATTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.44
Consensus pattern (27 bp):
ATCTTGCGTTTGTGTCCCAACATATTT
Found at i:2133446 original size:23 final size:23
Alignment explanation
Indices: 2133416--2133471 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
2133406 CACCTAAGTG
2133416 CCACATAGAAATGTCCCAAAGGA
1 CCACATAGAAATGTCCCAAAGGA
* *
2133439 CCACATAGAATTGTCCCGAAGGA
1 CCACATAGAAATGTCCCAAAGGA
* *
2133462 TCGCATAGAA
1 CCACATAGAA
2133472 CCCTCGACTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.16
Consensus pattern (23 bp):
CCACATAGAAATGTCCCAAAGGA
Found at i:2133649 original size:28 final size:28
Alignment explanation
Indices: 2133607--2133662 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
2133597 AGGGTATCTC
* *
2133607 CACGTAGAACTTTTTCACTAAACACATT
1 CACGTAAAACCTTTTCACTAAACACATT
* *
2133635 CACGTAAAACCTTTTCACTTAGCACATT
1 CACGTAAAACCTTTTCACTAAACACATT
2133663 ATCATATACA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.34, C:0.27, G:0.07, T:0.32
Consensus pattern (28 bp):
CACGTAAAACCTTTTCACTAAACACATT
Found at i:2134328 original size:20 final size:21
Alignment explanation
Indices: 2134296--2134340 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
2134286 AATTTCATCT
2134296 TTACTTATTGTATCGATA-CC
1 TTACTTATTGTATCGATACCC
2134316 TTAC-TATTGGTATCGATACCC
1 TTACTTATT-GTATCGATACCC
2134337 TTAC
1 TTAC
2134341 CAGTATTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.17
20 13 0.57
21 6 0.26
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.42
Consensus pattern (21 bp):
TTACTTATTGTATCGATACCC
Found at i:2135046 original size:8 final size:8
Alignment explanation
Indices: 2135033--2135074 Score: 75
Period size: 8 Copynumber: 5.2 Consensus size: 8
2135023 CATAGTATCA
2135033 TTCCATCT
1 TTCCATCT
2135041 TTCCATCT
1 TTCCATCT
2135049 TTCCATCT
1 TTCCATCT
2135057 TTCCATCT
1 TTCCATCT
*
2135065 TTCTATCT
1 TTCCATCT
2135073 TT
1 TT
2135075 GATAATAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 33 1.00
ACGTcount: A:0.12, C:0.33, G:0.00, T:0.55
Consensus pattern (8 bp):
TTCCATCT
Found at i:2138168 original size:110 final size:108
Alignment explanation
Indices: 2137987--2138336 Score: 347
Period size: 110 Copynumber: 3.2 Consensus size: 108
2137977 ACTAAGTTTG
* *
2137987 ATTTTCATAAGTTTCTTGATGATTTTTAAATGAGCTTTCAAAGAAACTAAGTCTGATTTTCA-AA
1 ATTTTCATAAGTTTCTTGATGATTTTTAAATGAGCTTTCAAAGAAACTAAGTTTGATTTTCAGAG
*
2138051 AGTTTCTTGATGATTTTTAAATGAGTTTTTAAAGAAACTAAGTCTT
66 A-TTTCTTGATGATTTTTAAA-GA-TTTTTAAAGAAACTAAGCCTT
2138097 ATTTTCATAAGTTTCTTGATGATTTTTAAATGAGCTTTCAAAGAAACTAAGTTTGATTTTCAGAG
1 ATTTTCATAAGTTTCTTGATGATTTTTAAATGAGCTTTCAAAGAAACTAAGTTTGATTTTCAGAG
* ** * * *
2138162 ATTTCTTGA-CATGATT--A-ATTTTTAAAGAAGCTAAACCTG
66 ATTTCTTGATGATTTTTAAAGATTTTTAAAGAAACTAAGCCTT
* * * * *
2138201 ATTTTCA-AAGGTTTCTTGATGATTATTTCTAATGA-ATTTTAAAGAAGCTAAGCATT-ATTTTC
1 ATTTTCATAA-GTTTCTTGATGATT-TTT-AAATGAGCTTTCAAAGAAACTAAG-TTTGATTTTC
* * * *
2138263 AGGGGTTTCTTGATGATTATTTCCAAAGAATTTTTAAAGAAGCTAAGCCTA
62 AGAGATTTCTTGATGATT-TTT--AAAG-ATTTTTAAAGAAACTAAGCCTT
* ***
2138314 ATTTTTAGGGGTTTCTTGATGAT
1 ATTTTCATAAGTTTCTTGATGAT
2138337 AACTGTAAAC
Statistics
Matches: 202, Mismatches: 24, Indels: 25
0.80 0.10 0.10
Matches are distributed among these distances:
103 2 0.01
104 38 0.19
105 35 0.17
106 9 0.04
107 3 0.01
109 4 0.02
110 69 0.34
111 3 0.01
113 39 0.19
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.43
Consensus pattern (108 bp):
ATTTTCATAAGTTTCTTGATGATTTTTAAATGAGCTTTCAAAGAAACTAAGTTTGATTTTCAGAG
ATTTCTTGATGATTTTTAAAGATTTTTAAAGAAACTAAGCCTT
Found at i:2138170 original size:55 final size:55
Alignment explanation
Indices: 2137955--2138158 Score: 333
Period size: 55 Copynumber: 3.7 Consensus size: 55
2137945 TTTTTTTATT
*
2137955 ATTTTTAAATGAGCTTTC--ATAAACTAAGTTTGATTTTCATAAGTTTCTTGATG
1 ATTTTTAAATGAGCTTTCAAAGAAACTAAGTTTGATTTTCATAAGTTTCTTGATG
* *
2138008 ATTTTTAAATGAGCTTTCAAAGAAACTAAGTCTGATTTTCAAAAGTTTCTTGATG
1 ATTTTTAAATGAGCTTTCAAAGAAACTAAGTTTGATTTTCATAAGTTTCTTGATG
* *
2138063 ATTTTTAAATGAGTTTTTAAAGAAACTAAGTCTT-ATTTTCATAAGTTTCTTGATG
1 ATTTTTAAATGAGCTTTCAAAGAAACTAAGT-TTGATTTTCATAAGTTTCTTGATG
2138118 ATTTTTAAATGAGCTTTCAAAGAAACTAAGTTTGATTTTCA
1 ATTTTTAAATGAGCTTTCAAAGAAACTAAGTTTGATTTTCA
2138159 GAGATTTCTT
Statistics
Matches: 138, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
53 18 0.13
54 2 0.01
55 117 0.85
56 1 0.01
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.44
Consensus pattern (55 bp):
ATTTTTAAATGAGCTTTCAAAGAAACTAAGTTTGATTTTCATAAGTTTCTTGATG
Found at i:2138324 original size:57 final size:57
Alignment explanation
Indices: 2138178--2138336 Score: 230
Period size: 56 Copynumber: 2.8 Consensus size: 57
2138168 TGACATGATT
* * ** * *
2138178 AATTTTTAAAGAAGCTAAACCTGATTTTCAAAGGTTTCTTGATGATTATTTCTAATG
1 AATTTTTAAAGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATGATTATTTCCAAAG
* *
2138235 AA-TTTTAAAGAAGCTAAGCATTATTTTCAGGGGTTTCTTGATGATTATTTCCAAAG
1 AATTTTTAAAGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATGATTATTTCCAAAG
*
2138291 AATTTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGAT
1 AATTTTTAAAGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATGAT
2138337 AACTGTAAAC
Statistics
Matches: 91, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
56 49 0.54
57 42 0.46
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (57 bp):
AATTTTTAAAGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATGATTATTTCCAAAG
Found at i:2138384 original size:58 final size:55
Alignment explanation
Indices: 2138181--2138391 Score: 185
Period size: 56 Copynumber: 3.7 Consensus size: 55
2138171 CATGATTAAT
* * ** * * *
2138181 TTTTAAAGAAGCTAAACCTGATTTTCAAAGGTTTCTTGATGATTATTTCTAATG-AA
1 TTTTAAAGAAGCT-AAGCTTATTTTCAGGGGTTTCTTGATGATAATGTC-AAAGAAA
* * *
2138237 TTTTAAAGAAGCTAAGCATTATTTTCAGGGGTTTCTTGATGATTATTTCCAAAGAAT
1 TTTTAAAGAAGCTAAGC-TTATTTTCAGGGGTTTCTTGATGATAATGT-CAAAGAAA
* *
2138294 TTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATAACTGT-AAACGAAAGA
1 TTTTAAAGAAGCTAAG-CTTATTTTCAGGGGTTTCTTGATGATAA-TGTCAAA-G-AA-A
* *
2138353 TTTT-AAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGAT
1 TTTTAAAGAAGCTAAGCTT-ATTTTCAGGGGTTTCTTGAT
2138392 TAGTAAGTCC
Statistics
Matches: 131, Mismatches: 15, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
55 3 0.02
56 46 0.35
57 45 0.34
58 33 0.25
59 4 0.03
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (55 bp):
TTTTAAAGAAGCTAAGCTTATTTTCAGGGGTTTCTTGATGATAATGTCAAAGAAA
Found at i:2140185 original size:23 final size:22
Alignment explanation
Indices: 2140154--2140217 Score: 56
Period size: 23 Copynumber: 2.8 Consensus size: 22
2140144 TTCAAATTAA
* *
2140154 ATATTCAAACCATTCAAACAAAT
1 ATATCCAAA-CATTCAAACAAAC
* *
2140177 ATATCCAAACATCCAAAACACAC
1 ATATCCAAACATTC-AAACAAAC
*
2140200 AAATCCAAATCATTCAAA
1 ATATCCAAA-CATTCAAA
2140218 ATATTTTAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
22 4 0.12
23 25 0.76
24 4 0.12
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (22 bp):
ATATCCAAACATTCAAACAAAC
Found at i:2141644 original size:12 final size:13
Alignment explanation
Indices: 2141627--2141659 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
2141617 ATGGGAAAAA
2141627 TTTGAAAACAAT-
1 TTTGAAAACAATG
2141639 TTTGAAAACAATG
1 TTTGAAAACAATG
2141652 TTTGAAAA
1 TTTGAAAA
2141660 ATCATAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.33
Consensus pattern (13 bp):
TTTGAAAACAATG
Found at i:2142399 original size:22 final size:22
Alignment explanation
Indices: 2142374--2142418 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2142364 CCCCCTAACT
2142374 ATTAGCATAGAAAGCATTCAAA
1 ATTAGCATAGAAAGCATTCAAA
2142396 ATTAGCATAGAAAGCATTCAAA
1 ATTAGCATAGAAAGCATTCAAA
2142418 A
1 A
2142419 ATGTCGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.22
Consensus pattern (22 bp):
ATTAGCATAGAAAGCATTCAAA
Found at i:2144232 original size:12 final size:12
Alignment explanation
Indices: 2144215--2144239 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2144205 ATGATGGCTA
2144215 TCCAACGTCATG
1 TCCAACGTCATG
2144227 TCCAACGTCATG
1 TCCAACGTCATG
2144239 T
1 T
2144240 GTATTTACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.32, G:0.16, T:0.28
Consensus pattern (12 bp):
TCCAACGTCATG
Found at i:2147630 original size:20 final size:20
Alignment explanation
Indices: 2147605--2147655 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
2147595 ATATGGGGTG
*
2147605 TATCGGTACATATAGGAGTA
1 TATCGGTACATACAGGAGTA
*
2147625 TATCGGTACATACAGGAGTG
1 TATCGGTACATACAGGAGTA
2147645 TATCGGTACAT
1 TATCGGTACAT
2147656 CCCTTTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.29
Consensus pattern (20 bp):
TATCGGTACATACAGGAGTA
Found at i:2148480 original size:40 final size:39
Alignment explanation
Indices: 2148420--2148516 Score: 124
Period size: 40 Copynumber: 2.5 Consensus size: 39
2148410 ACGATTCTAG
** *
2148420 AAAGAGTTGGATCAGTATCACC-TGGGCTCATCCATCACA
1 AAAGAGTTGGATCAACATCACCTTGGG-TCAACCATCACA
*
2148459 TAAGGAGTTGGATCAACATCACCTTGGGTCAACCATCACA
1 -AAAGAGTTGGATCAACATCACCTTGGGTCAACCATCACA
*
2148499 AAAGAGTTGGGTCAACAT
1 AAAGAGTTGGATCAACAT
2148517 TTTCAAAAGA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
39 16 0.32
40 30 0.60
41 4 0.08
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.23
Consensus pattern (39 bp):
AAAGAGTTGGATCAACATCACCTTGGGTCAACCATCACA
Found at i:2150615 original size:3 final size:3
Alignment explanation
Indices: 2150607--2150681 Score: 114
Period size: 3 Copynumber: 25.0 Consensus size: 3
2150597 ATTGATTTAT
* *
2150607 TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
2150655 TAA ATA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
2150682 AATCTATTAA
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:2150689 original size:12 final size:12
Alignment explanation
Indices: 2150607--2150690 Score: 88
Period size: 12 Copynumber: 7.2 Consensus size: 12
2150597 ATTGATTTAT
*
2150607 TTATTATTATTA
1 TTATTATAATTA
2150619 TTATTATAATTA
1 TTATTATAATTA
2150631 TTA-T-T-ATTA
1 TTATTATAATTA
2150640 TTATTATAATTA
1 TTATTATAATTA
*
2150652 TTA-TAAATATTA
1 TTATTATA-ATTA
*
2150664 TTATTATTATTA
1 TTATTATAATTA
2150676 TTATTA-AATCTA
1 TTATTATAAT-TA
2150688 TTA
1 TTA
2150691 AATATATATA
Statistics
Matches: 61, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
9 7 0.11
10 2 0.03
11 7 0.11
12 43 0.70
13 2 0.03
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (12 bp):
TTATTATAATTA
Found at i:2155338 original size:22 final size:22
Alignment explanation
Indices: 2155308--2155356 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
2155298 GAATCTGAAA
*
2155308 TGAACCAGCTGATTGCTGAACT
1 TGAAGCAGCTGATTGCTGAACT
2155330 TGAAGCAGCTGATTGCTGAACT
1 TGAAGCAGCTGATTGCTGAACT
2155352 TGAAG
1 TGAAG
2155357 TCAGAGGCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (22 bp):
TGAAGCAGCTGATTGCTGAACT
Found at i:2156102 original size:15 final size:15
Alignment explanation
Indices: 2156082--2156113 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2156072 ATCAATACCT
2156082 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
2156097 TTTTGCATACATTCA
1 TTTTGCATACATGCA
2156112 TT
1 TT
2156114 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:2163806 original size:16 final size:16
Alignment explanation
Indices: 2163780--2163824 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
2163770 TTTGAATACA
*
2163780 ATTCTATTTATTTCAAG
1 ATTCAATTTATTT-AAG
*
2163797 -TTCAATTTATTTGAG
1 ATTCAATTTATTTAAG
2163812 ATTCAATTTATTT
1 ATTCAATTTATTT
2163825 TCGAAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.56
Consensus pattern (16 bp):
ATTCAATTTATTTAAG
Found at i:2164753 original size:83 final size:83
Alignment explanation
Indices: 2164609--2165166 Score: 990
Period size: 83 Copynumber: 6.7 Consensus size: 83
2164599 ATTAGCTGGA
* * * *
2164609 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTCCTTTGAGTTATCTGATCTGGTTTGGTAAA
1 AAGAGGAATGGGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAA
*
2164674 ACTAATCATTGAATTTGG
66 ACCAATCATTGAATTTGG
*
2164692 AAGAGGAATGGGCTAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAA
1 AAGAGGAATGGGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAA
2164757 ACCAATCATTGAATTTGG
66 ACCAATCATTGAATTTGG
** * * *
2164775 AAGAATAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGGTTTGGTAAA
1 AAGAGGAATGGGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAA
2164840 ACCAATCATTGAATTTGG
66 ACCAATCATTGAATTTGG
*
2164858 AAGAGGAATGGGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAA
1 AAGAGGAATGGGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAA
2164923 ACCAATCATTGAATTTGG
66 ACCAATCATTGAATTTGG
2164941 AAGAGGAATGGGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAA
1 AAGAGGAATGGGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAA
2165006 ACCAATCATTGAATTTGG
66 ACCAATCATTGAATTTGG
2165024 AAGAGGAATGGGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAA
1 AAGAGGAATGGGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAA
*
2165089 ACCAATCATTGAATTTAG
66 ACCAATCATTGAATTTGG
*
2165107 AAGAGGAATGGGCTAATAGCATCTTCTGGAAGTGTTATTTGAGTTATCTGATCTGGTTTG
1 AAGAGGAATGGGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
2165167 ATATGAAACC
Statistics
Matches: 456, Mismatches: 19, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 456 1.00
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.36
Consensus pattern (83 bp):
AAGAGGAATGGGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAA
ACCAATCATTGAATTTGG
Found at i:2166207 original size:113 final size:113
Alignment explanation
Indices: 2166045--2166301 Score: 354
Period size: 113 Copynumber: 2.3 Consensus size: 113
2166035 TTCCAGTTCG
* * *
2166045 AGTTCATAATGAGAAGAACTCATTTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATAAGAAGAACTTGTTC
* * ***
2166110 AACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTTTGCC-AGAGAA
66 AACCCTTTGCTCAAATCCATCACTTGATGGATCAGCAGCGCCTA-AGAA
* *
2166158 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATAAGAAGAACTTGTTC
** * * *
2166223 AACCCTTTGCTTGAATTCATCATTTGATGGATCAGCAGCGCCTAAGAG
66 AACCCTTTGCTCAAATCCATCACTTGATGGATCAGCAGCGCCTAAGAA
*
2166271 AGTTCATAATGAGAAGAACTCATCTAAAGAA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAA
2166302 CTTGTTTAAC
Statistics
Matches: 127, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
113 126 0.99
114 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATAAGAAGAACTTGTTC
AACCCTTTGCTCAAATCCATCACTTGATGGATCAGCAGCGCCTAAGAA
Found at i:2166341 original size:87 final size:86
Alignment explanation
Indices: 2166211--2166388 Score: 243
Period size: 87 Copynumber: 2.1 Consensus size: 86
2166201 TCATAATAAG
* * *
2166211 AAGAACTTGTTTAACCCTTTGCTTGAATTCATCATTTGATGGATCAGCAGCGCCTA-AGAGAGTT
1 AAGAACTTGTTTAACCCTTTGCTTAAATCCATCATTTGATGGATCAGCAGCGCC-AGAGAAAGTT
2166275 CATAATGAGAAGAACTCATCTA
65 CATAATGAGAAGAACTCATCTA
****
2166297 AAGAACTTGTTTAACCCTTTTG-TTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGT
1 AAGAACTTGTTTAACCC-TTTGCTT-AAATCCATCATTTGATGGATCAGCAGCGCCAGAGAAAGT
*
2166361 TCATAATGAGAAGAACTCATCTG
64 TCATAATGAGAAGAACTCATCTA
2166384 AAGAA
1 AAGAA
2166389 AGAAGAAGAA
Statistics
Matches: 81, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
86 20 0.25
87 61 0.75
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (86 bp):
AAGAACTTGTTTAACCCTTTGCTTAAATCCATCATTTGATGGATCAGCAGCGCCAGAGAAAGTTC
ATAATGAGAAGAACTCATCTA
Found at i:2166455 original size:200 final size:199
Alignment explanation
Indices: 2166098--2166501 Score: 585
Period size: 200 Copynumber: 2.0 Consensus size: 199
2166088 TCATAATGAG
* *
2166098 AAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTTTGCCAGAGAAAGTTC
1 AAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTGCCAGAGAAAGTTC
* * *
2166163 ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTTAACCC
66 ATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAATTCATAATAAGAAGAACTTGTTCAACCC
** * *
2166228 TTTGCTTGAATTCATCATTTGATGGATCAGCAGCGCCTA-AGAGAGTTCATAATGAGAAGAACTC
131 TTTGCTCAAATCCATCATTTGATGGATCAGCAGCGCC-AGAGAAAGTTCATAATGAGAAGAACTC
2166292 ATCTA
195 ATCTA
* * * *
2166297 AAGAACTTGTTTAACCCTTTTGTTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTT
1 AAGAACTTGTTCAA-CCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTGCCAGAGAAAGTT
* * *
2166362 CATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAATC
65 CATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAATTCATAATAAGAAGAACTTGTTCAACC
* ****
2166427 TTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTC
130 CTTTGCTCAAATCCATCATTTGATGGATCAGCAGCGCCAGAGAAAGTTCATAATGAGAAGAACTC
*
2166492 ATCTG
195 ATCTA
2166497 AAGAA
1 AAGAA
2166502 GGAAGAAGAA
Statistics
Matches: 181, Mismatches: 22, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
199 13 0.07
200 168 0.93
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.29
Consensus pattern (199 bp):
AAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTGCCAGAGAAAGTTC
ATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAATTCATAATAAGAAGAACTTGTTCAACCC
TTTGCTCAAATCCATCATTTGATGGATCAGCAGCGCCAGAGAAAGTTCATAATGAGAAGAACTCA
TCTA
Found at i:2166511 original size:113 final size:112
Alignment explanation
Indices: 2166297--2166765 Score: 644
Period size: 113 Copynumber: 4.2 Consensus size: 112
2166287 AACTCATCTA
* * *
2166297 AAGAACTTGTTTAACCCTTTTGTTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTT
1 AAGAATTTGTTCAA-CCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTT
*
2166362 CATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAATTCATAATGAG
65 CATAATGAGAAGAACTCATCTGAAG-AAGAAGAAGAAATTCATAATAAG
*
2166411 AAGAATTTGTTCAATCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTC
1 AAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTC
*
2166476 ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAG
66 ATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAATTCATAATAAG
* * * * * * * *
2166524 AAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTGCCAG-GTAGAGTT
1 AAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAG-AAAGTT
* ** *
2166588 CATAATGAGAAGAACTCGTCAT-CTGAAGAAGAAGAAATTCATAATGAG
65 CATAATGAGAAGAACTCATC-TGAAGAAGAAGAAGAAATTCATAATAAG
* *
2166636 AAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGAGCAGCTTTTCCAGAG-AAGTTC
1 AAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTC
2166700 ATAATGAGAAGAACTCATCTGAAGAAGAAGAAG---TTCATAATAAG
66 ATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAATTCATAATAAG
** *
2166744 AAGAGCTTGTTCAACTTTTTGC
1 AAGAATTTGTTCAACCTTTTGC
2166766 ATAATTCTAT
Statistics
Matches: 313, Mismatches: 37, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
108 29 0.09
110 1 0.00
111 33 0.11
112 69 0.22
113 168 0.54
114 13 0.04
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (112 bp):
AAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTC
ATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAATTCATAATAAG
Found at i:2166588 original size:313 final size:313
Alignment explanation
Indices: 2166009--2166604 Score: 960
Period size: 313 Copynumber: 1.9 Consensus size: 313
2165999 GCAAAGATTT
**** *
2166009 AAATCCATCATTCAATGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATTTGAAG
1 AAATCCATCATTCAATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
2166074 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATG
66 AAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATG
*
2166139 GATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
131 GATCAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* * *
2166204 TAATAAGAAGAACTTGTTTAACCCTTTGCTTGAATTCATCATTTGATGGATCAGCAGCGCCTAAG
196 TAATAAGAAGAACTTGTTCAACCCTTTGCTTAAATTCATCATTTGATGGATCAACAGCGCCTAAG
2166269 AGAGTTCATAATGAGAAGAACTCATCTAAAGAACTTGTTTAACCCTTTTGTTC
261 AGAGTTCATAATGAGAAGAACTCATCTAAAGAACTTGTTTAACCCTTTTGTTC
** * *
2166322 AAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCATTCAATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* *
2166387 AAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAATCTTTTGCTCAAATCCATCATTTGATG
66 AAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATG
*
2166452 GATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
131 GATCAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* * * * ** *
2166517 TAATAAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTGCC-AGG
196 TAATAAGAAGAACTTGTTCAACCCTTTGCTTAAATTCATCATTTGATGGATCAACAGCGCCTAAG
2166581 TAGAGTTCATAATGAGAAGAACTC
261 -AGAGTTCATAATGAGAAGAACTC
2166605 GTCATCTGAA
Statistics
Matches: 258, Mismatches: 24, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
312 2 0.01
313 256 0.99
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.29
Consensus pattern (313 bp):
AAATCCATCATTCAATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
AAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATG
GATCAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
TAATAAGAAGAACTTGTTCAACCCTTTGCTTAAATTCATCATTTGATGGATCAACAGCGCCTAAG
AGAGTTCATAATGAGAAGAACTCATCTAAAGAACTTGTTTAACCCTTTTGTTC
Found at i:2166746 original size:17 final size:17
Alignment explanation
Indices: 2166692--2166747 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
2166682 GCTTTTCCAG
*
2166692 AGAAGTTCATAATGAGA
1 AGAAGTTCATAATAAGA
* *
2166709 AGAA-CTCATCTGAAGAAGA
1 AGAAGTTCA--T-AATAAGA
2166728 AGAAGTTCATAATAAGA
1 AGAAGTTCATAATAAGA
2166745 AGA
1 AGA
2166748 GCTTGTTCAA
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
16 3 0.10
17 13 0.43
18 2 0.07
19 9 0.30
20 3 0.10
ACGTcount: A:0.50, C:0.09, G:0.21, T:0.20
Consensus pattern (17 bp):
AGAAGTTCATAATAAGA
Found at i:2166884 original size:84 final size:82
Alignment explanation
Indices: 2166730--2166913 Score: 199
Period size: 84 Copynumber: 2.2 Consensus size: 82
2166720 GAAGAAGAAG
* * * * * * * *
2166730 AAGTTCATAATAAGAAGAGCTTGTTCAACTTTTTGCATAATTCTATCATAGAAGGAGATAGATTA
1 AAGTTCATAATAAGAAGAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAGGAAAAAGATCA
*
2166795 GCATCAGCCTTTCCAG-AGA
66 ACATCAGCC---CCAGTAGA
* * * *
2166814 AAGTTCATAATGAGAAGAGCTTATTTAACCTTTTGAATGACTCTATCACAGAAGGAAAAAGGTCA
1 AAGTTCATAATAAGAAGAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAGGAAAAAGATCA
* *
2166879 ACATCATCCCCAGTGGA
66 ACATCAGCCCCAGTAGA
2166896 AAGTTCATAATAAGAAGA
1 AAGTTCATAATAAGAAGA
2166914 ACTCATCTGA
Statistics
Matches: 83, Mismatches: 16, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
81 4 0.05
82 19 0.23
84 60 0.72
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.28
Consensus pattern (82 bp):
AAGTTCATAATAAGAAGAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAGGAAAAAGATCA
ACATCAGCCCCAGTAGA
Done.