Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005581.1 Hibiscus syriacus cultivar Beakdansim tig00012952_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: 117071
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:2246 original size:9 final size:9
Alignment explanation
Indices: 2232--2267 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
2222 TGCACTCATT
2232 TAATATATA
1 TAATATATA
2241 TAATATATA
1 TAATATATA
*
2250 TATTATATA
1 TAATATATA
2259 T-ATATATA
1 TAATATATA
2267 T
1 T
2268 CATTCTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 7 0.28
9 18 0.72
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
TAATATATA
Found at i:2250 original size:11 final size:11
Alignment explanation
Indices: 2234--2264 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2224 CACTCATTTA
2234 ATATATATAAT
1 ATATATATAAT
*
2245 ATATATATTAT
1 ATATATATAAT
2256 ATATATATA
1 ATATATATA
2265 TATCATTCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
ATATATATAAT
Found at i:2280 original size:2 final size:2
Alignment explanation
Indices: 2234--2267 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2224 CACTCATTTA
2234 AT AT AT AT A- AT AT AT AT AT -T 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
2268 CATTCTAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2656 original size:15 final size:15
Alignment explanation
Indices: 2636--2669 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2626 TATATGTTTA
2636 AAAAATAAT-TGACT
1 AAAAATAATATGACT
2650 CAAAAATAATATGACT
1 -AAAAATAATATGACT
2666 AAAA
1 AAAA
2670 TATTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.62, C:0.09, G:0.06, T:0.24
Consensus pattern (15 bp):
AAAAATAATATGACT
Found at i:23162 original size:15 final size:15
Alignment explanation
Indices: 23142--23173 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
23132 TACCTAACTG
*
23142 AATTTCTATCTCTTT
1 AATTTCTAACTCTTT
23157 AATTTCTAACTCTTT
1 AATTTCTAACTCTTT
23172 AA
1 AA
23174 AAAAAAGAAA
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:0.28, C:0.19, G:0.00, T:0.53
Consensus pattern (15 bp):
AATTTCTAACTCTTT
Found at i:25173 original size:21 final size:21
Alignment explanation
Indices: 25134--25173 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
25124 TAACAAAGGT
*
25134 AGTACCGATACTCCCTATAGG
1 AGTACCGATACTCCATATAGG
25155 AGTACCGATAC-CCTATATA
1 AGTACCGATACTCC-ATATA
25174 CTGGGCAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.25
Consensus pattern (21 bp):
AGTACCGATACTCCATATAGG
Found at i:28166 original size:21 final size:20
Alignment explanation
Indices: 28117--28167 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
28107 CATCTTTATT
* *
28117 TTTTAACTTTTCATATATAA
1 TTTTAACTATTCATAAATAA
*
28137 TTGTAAACTATTCATAAATAAA
1 TT-TTAACTATTCATAAAT-AA
28159 TTTTAACTA
1 TTTTAACTA
28168 AACACAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 2 0.08
21 19 0.76
22 4 0.16
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.47
Consensus pattern (20 bp):
TTTTAACTATTCATAAATAA
Found at i:28337 original size:3 final size:3
Alignment explanation
Indices: 28322--28412 Score: 164
Period size: 3 Copynumber: 30.3 Consensus size: 3
28312 TCTTTTTGTA
* *
28322 TTC TTC TTA TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TAC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
28370 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
28413 CGATTTTCTC
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 84 1.00
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:29161 original size:30 final size:30
Alignment explanation
Indices: 29125--29185 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
29115 ATATATTTTT
* * *
29125 GCCCATTACGACACGTGGAAAAATTAATTG
1 GCCCATTAAGACAAGTGAAAAAATTAATTG
*
29155 GCCCATTAAGTCAAGTGAAAAAATTAATTG
1 GCCCATTAAGACAAGTGAAAAAATTAATTG
29185 G
1 G
29186 TCCAATAGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (30 bp):
GCCCATTAAGACAAGTGAAAAAATTAATTG
Found at i:30363 original size:206 final size:204
Alignment explanation
Indices: 29936--30484 Score: 762
Period size: 203 Copynumber: 2.7 Consensus size: 204
29926 GATCGTTCCA
* * *
29936 TGGATCCAATATCATTGCCGGCTAACTGTTGAGGTGCACTCTGGTGATGAAA-TTTTGTTGAAGT
1 TGGATCCAATATCATTGCCGGCAAACTGGTGAGGTGCACTCTGGTGATGAAAGTTTTGTTGAGGT
* * ** * * * *
30000 TGATAAGAATTTAGGAAGGGATCGGCATTGGAATGACAAATTAGACCTAAATCATGAGTTGAATG
66 TGATAAGAATTTAGGACGAGATCGGCATTGGAATGATGAATGAAACCTAAATCATCAGTGGAATG
* * *
30065 ACCAGGTTTTGTTCCAGGTATTGTCCGTGGATCCATACAAGGTCTGTAAGGCAATGATCTTACCA
131 AACAGGTTTTGTTCCAGGTACTGCCCGTGGATCCATACAAGGTCTGTAAGGCAATGATCTTACCA
30130 TTCTTGAAG
196 TTCTTGAAG
*
30139 TGGATCCAATATCATTGCCGGCAAACTGGTGAGGTGAACTCTGGTGATGAAAGTTTTGTTG-GGT
1 TGGATCCAATATCATTGCCGGCAAACTGGTGAGGTGCACTCTGGTGATGAAAGTTTTGTTGAGGT
* * * * *
30203 CGATAAGAATTTAGGACGAGATTGGCATTGGAGTGATGAATGACACCTACATCATCAGTGGAATG
66 TGATAAGAATTTAGGACGAGATCGGCATTGGAATGATGAATGAAACCTAAATCATCAGTGGAATG
** * *
30268 AACAGGTTTTGTTGAAGTAGGTACTGCCCGTGGATCCGTATAAGGTCTGTAAGGCAATGATCTTA
131 AACAGGTTTTGTT---CCAGGTACTGCCCGTGGATCCATACAAGGTCTGTAAGGCAATGATCTTA
*
30333 CCATTGTTGAAG
193 CCATTCTTGAAG
* *
30345 TGGATCCAATAGCATTGCCGGCAAACTGGTGAGGAGCACTCTGGTGATGAAAGTTTTGTTGAGGT
1 TGGATCCAATATCATTGCCGGCAAACTGGTGAGGTGCACTCTGGTGATGAAAGTTTTGTTGAGGT
* * * *
30410 TGATAAGAATTTAGGAC-AGGATCAGCATTGGATTGATGAATGAAACCTATATCATCAATGGAAT
66 TGATAAGAATTTAGGACGA-GATCGGCATTGGAATGATGAATGAAACCTAAATCATCAGTGGAAT
30474 GAACAGGTTTT
130 GAACAGGTTTT
30485 TCTTCCTTCG
Statistics
Matches: 306, Mismatches: 34, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
203 116 0.38
204 8 0.03
206 113 0.37
207 69 0.23
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (204 bp):
TGGATCCAATATCATTGCCGGCAAACTGGTGAGGTGCACTCTGGTGATGAAAGTTTTGTTGAGGT
TGATAAGAATTTAGGACGAGATCGGCATTGGAATGATGAATGAAACCTAAATCATCAGTGGAATG
AACAGGTTTTGTTCCAGGTACTGCCCGTGGATCCATACAAGGTCTGTAAGGCAATGATCTTACCA
TTCTTGAAG
Found at i:31038 original size:177 final size:173
Alignment explanation
Indices: 30742--31113 Score: 471
Period size: 177 Copynumber: 2.1 Consensus size: 173
30732 CAGCATTTGG
* * * * * * *
30742 CCTCTCAGATGGTACGGAGGTAGCACTCGTCCCTAATTATAAAAGAACAATGTAATGTAAAATTC
1 CCTCTCAGAAGGTACAGAGGTAACACTCATACCTAATTATAAAAGAAAAATATAATGTAAAATTC
* *
30807 CAGTAGATCAATAATAAAAAATATGGAATTCACAGAAACATAGTTTGTTTTCACCATCAT-GCTC
66 CAGTAGATCAATAATAAAAAATATGGAATTCACAGAAACAAAGTTTGCTTTCACCATC-TCGCTC
* * *
30871 TCGT-ACATACCAACATCGCCATTTTGCTGAGTTGTTGGAGTAGA
130 TC-TAACATACCAACATCACCATCTTGCTGAATTGTTGGAGTAGA
*
30915 CCTCTCAGAAGGTACAGAGGTAACACTCATACCTAATTATAAAAGAAGAAACATATGATGTAAAA
1 CCTCTCAGAAGGTACAGAGGTAACACTCATACCTAATTATAAAAG-A-AAA-ATATAATGTAAAA
* *
30980 TTCCAGTAGCTCAATAGTCAAAAGAA-ATGGAATTCACAGAAACAAAGTTTGCTTTCACCATCTC
63 TTCCAGTAGATCAATAAT-AAAA-AATATGGAATTCACAGAAACAAAGTTTGCTTTCACCATCTC
* * *
31044 GCTTTCTAACATACCAACGTCACCATCTTGCTGAATTGTTGGAGTAGG
126 GCTCTCTAACATACCAACATCACCATCTTGCTGAATTGTTGGAGTAGA
* * *
31092 CTTCTCAGAGGGAACAGAGGTA
1 CCTCTCAGAAGGTACAGAGGTA
31114 GCAGTCATCC
Statistics
Matches: 171, Mismatches: 21, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
173 40 0.23
174 1 0.01
175 2 0.01
176 29 0.17
177 97 0.57
178 2 0.01
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (173 bp):
CCTCTCAGAAGGTACAGAGGTAACACTCATACCTAATTATAAAAGAAAAATATAATGTAAAATTC
CAGTAGATCAATAATAAAAAATATGGAATTCACAGAAACAAAGTTTGCTTTCACCATCTCGCTCT
CTAACATACCAACATCACCATCTTGCTGAATTGTTGGAGTAGA
Found at i:31643 original size:30 final size:30
Alignment explanation
Indices: 31602--31672 Score: 106
Period size: 30 Copynumber: 2.4 Consensus size: 30
31592 TGTTGGAGTG
* * *
31602 GGCCTCACAGATGGTACATACGTAGTACTC
1 GGCCTCTCAGATGGTACATACATAGCACTC
31632 GGCCTCTCAGATGGTACATACATAGCACTC
1 GGCCTCTCAGATGGTACATACATAGCACTC
*
31662 AGCCTCTCAGA
1 GGCCTCTCAGA
31673 CAGTACAGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.23
Consensus pattern (30 bp):
GGCCTCTCAGATGGTACATACATAGCACTC
Found at i:31679 original size:30 final size:30
Alignment explanation
Indices: 31615--31679 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
31605 CTCACAGATG
* * * **
31615 GTACATACGTAGTACTCGGCCTCTCAGATG
1 GTACATACATAGCACTCAGCCTCTCAGACA
31645 GTACATACATAGCACTCAGCCTCTCAGACA
1 GTACATACATAGCACTCAGCCTCTCAGACA
31675 GTACA
1 GTACA
31680 GAGGCAGCAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.23
Consensus pattern (30 bp):
GTACATACATAGCACTCAGCCTCTCAGACA
Found at i:32020 original size:177 final size:177
Alignment explanation
Indices: 31663--32027 Score: 462
Period size: 177 Copynumber: 2.1 Consensus size: 177
31653 ATAGCACTCA
* ** * * *
31663 GCCTCTCAGACAGTACAGAGGCAGCACTTGTACCTAATTATAAAAGAAGAAACATGTGATGTAAA
1 GCCTCTCAGACAGTACACAGGCAGCACCCGTACCTAATAATAAAAGAAGAAACACGTGACGTAAA
* * *
31728 ATTCCATTAGCTCAATAGTCAAAAGAAAGGGAATTCACAGAAACATAGTTTGCTTGCACCATCTT
66 ATTCCAGTAGCTCAAGAGTCAAAAGAAAGGGAATTCACAGAAACATAGTTTGCTTGCACCATCTC
* * * *
31793 GCTCTCTAACATACCAACATCACCCTCTTGCCGAGTTCTTTGAATAG
131 ACTCTCTAACATACCAACATCACCATATTGCCGAGTTATTTGAATAG
* * * *
31840 GCCTCACAGACAGTACACAGGTAGCCCCCGTACCTAATAATAAAAGAAGAAACACGTGACGTAAT
1 GCCTCTCAGACAGTACACAGGCAGCACCCGTACCTAATAATAAAAGAAGAAACACGTGACGTAAA
* * * * * *
31905 ATTCCAGTAGCTTAAGAGTCGAAAGAAATGGACTTTACAGAAACATAGTTTGCTTTCACCATCTC
66 ATTCCAGTAGCTCAAGAGTCAAAAGAAAGGGAATTCACAGAAACATAGTTTGCTTGCACCATCTC
* * * **
31970 ACTCTCTTACATACCGATATCACCATATTGCTTAG-TATTTGAAGTAG
131 ACTCTCTAACATACCAACATCACCATATTGCCGAGTTATTTGAA-TAG
32017 GCCTCTCAGAC
1 GCCTCTCAGAC
32028 GGCATAGAGG
Statistics
Matches: 158, Mismatches: 29, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
176 7 0.04
177 151 0.96
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (177 bp):
GCCTCTCAGACAGTACACAGGCAGCACCCGTACCTAATAATAAAAGAAGAAACACGTGACGTAAA
ATTCCAGTAGCTCAAGAGTCAAAAGAAAGGGAATTCACAGAAACATAGTTTGCTTGCACCATCTC
ACTCTCTAACATACCAACATCACCATATTGCCGAGTTATTTGAATAG
Found at i:32614 original size:42 final size:42
Alignment explanation
Indices: 32547--32756 Score: 312
Period size: 42 Copynumber: 5.0 Consensus size: 42
32537 TTGCAGCGTG
* * *
32547 TCGTTTGCGCTTCTCAAGACATACATTTCTTCTTTCAGCCTC
1 TCGTTTGCGCTTCCCAGGACGTACATTTCTTCTTTCAGCCTC
* * *
32589 TCGTTTGCGCTTCCCAGGTCGTACATTTCTTCTCTCAGTCTC
1 TCGTTTGCGCTTCCCAGGACGTACATTTCTTCTTTCAGCCTC
* *
32631 TCGTTTGCGCTTCCCAAGACGAACATTTCTTCTTTCAGCCTC
1 TCGTTTGCGCTTCCCAGGACGTACATTTCTTCTTTCAGCCTC
* * *
32673 TCGTTTGCGCTTCCCAGGACGAACATTGCTTATTTCAGCCTC
1 TCGTTTGCGCTTCCCAGGACGTACATTTCTTCTTTCAGCCTC
*
32715 TCGTTCGCGCTTCCCAGGACGTACATTTCTTCTTTCAGCCTC
1 TCGTTTGCGCTTCCCAGGACGTACATTTCTTCTTTCAGCCTC
32757 ATCACACCAA
Statistics
Matches: 150, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 150 1.00
ACGTcount: A:0.14, C:0.33, G:0.16, T:0.37
Consensus pattern (42 bp):
TCGTTTGCGCTTCCCAGGACGTACATTTCTTCTTTCAGCCTC
Found at i:34789 original size:33 final size:33
Alignment explanation
Indices: 34747--34846 Score: 173
Period size: 33 Copynumber: 3.0 Consensus size: 33
34737 CTAATGCGGA
34747 CCAAAATAAACAAATTCAAGGACTAATTTGGAC
1 CCAAAATAAACAAATTCAAGGACTAATTTGGAC
34780 CCAAAATAAACAAATTCAAGGACTAATTTGGAC
1 CCAAAATAAACAAATTCAAGGACTAATTTGGAC
* * *
34813 CCAAAATAAACAAATCCAGGGACTAATGTGGAC
1 CCAAAATAAACAAATTCAAGGACTAATTTGGAC
34846 C
1 C
34847 AACAAATTAG
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 64 1.00
ACGTcount: A:0.47, C:0.20, G:0.14, T:0.19
Consensus pattern (33 bp):
CCAAAATAAACAAATTCAAGGACTAATTTGGAC
Found at i:35618 original size:20 final size:21
Alignment explanation
Indices: 35589--35629 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
35579 TCAATCTTCT
*
35589 ATTTTCAGAACA-AAAAATGA
1 ATTTTAAGAACAGAAAAATGA
*
35609 ATTTTAAGAAGAGAAAAATGA
1 ATTTTAAGAACAGAAAAATGA
35630 CCTTTGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.56, C:0.05, G:0.15, T:0.24
Consensus pattern (21 bp):
ATTTTAAGAACAGAAAAATGA
Found at i:36012 original size:20 final size:21
Alignment explanation
Indices: 35983--36023 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
35973 TCAATCTTCT
*
35983 ATTTTCAGAACA-AAAAATGA
1 ATTTTAAGAACAGAAAAATGA
*
36003 ATTTTAAGAAGAGAAAAATGA
1 ATTTTAAGAACAGAAAAATGA
36024 CCTTTGACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.56, C:0.05, G:0.15, T:0.24
Consensus pattern (21 bp):
ATTTTAAGAACAGAAAAATGA
Found at i:36238 original size:392 final size:398
Alignment explanation
Indices: 35000--36832 Score: 2136
Period size: 392 Copynumber: 4.6 Consensus size: 398
34990 ATGATGAAAT
* * *
35000 TACCTCCAATGCTCAAGAATTCTTTGTTGGCACACTGCCTTAGTGCCTGTGATAAGGAGGCCATG
1 TACCTCCAATGCTCAAGAATTCTCTGTTGACACACTGCCTTAGTGCCTGTGATACGGAGGCCATG
* * * *
35065 ATTTCTCAAATAAGCTTTCAGTTCTTTCAAGCTTAAGCTTTCAAAGTCACCCCCTTCTATGGAAC
66 GTTTCTCAAATAAGCTTTGAGTTCTTTCAAGCTTAAGCTTTCTAAGTCACCTCCTTCTATGGAAC
* * * * * *
35130 A-ACAGAAACATATATTGTAAGGGCATTTTTTGGGATCAAATTCAATCTTCTATTTTCA-AACAA
131 ACA-AGGATCATAAATTGTAACGGTA-TTTTTCGGATCAAATTCAATCTTCTATTTTCAGAACAA
* * * * * *
35193 AAAATGAATTCTACGAAGAGAAAGATGACCTTTGAGAATTGCAATGACTTGATTGCAGAGAGAAT
194 AAAATGAATTCTAAGAAGAGAAAAATGACCTTTGAGAATAGCAACGACTCGATTGCAGAGAGATT
* * * *
35258 CATCGTTCTCAGTCCGGTCATTATAGTTCACATTGTTCCTTTCCTCTTCCTCTTCTTCCCCAGTT
259 CATCGTTCTC--T--GGTC---ATAGATC-CATTGTTCCCTTCCTCTTTCTCTTCTTCCTCAGTT
* * * ** **** *
35323 TCATCTCCACTGATGATATCAAAATT-AATCA-AAATTGGGGAGGGGGGGGGGGC-AAAATAATT
316 TCAACTCCACTGATGATATGAAAATTAAATCAGACA-T---GAAAGGGGGAAAACTGAAATAATT
* *
35385 GAAATAGAAATAGG-AATGTAAA
377 GAAATTGAAATAGGAAAT-AAAA
* * *
35407 TACCTCCAATGCTCAAGAATTCTCTGTTGACACATTGCCTTACTGCCTGTGATACGAAGGCCATG
1 TACCTCCAATGCTCAAGAATTCTCTGTTGACACACTGCCTTAGTGCCTGTGATACGGAGGCCATG
* *
35472 ATTTCTCAAATAAGCTTTGAGTTCTTTCATGCTTAAGCTTTCTAAGTCACCTCCTTCTATGGAAC
66 GTTTCTCAAATAAGCTTTGAGTTCTTTCAAGCTTAAGCTTTCTAAGTCACCTCCTTCTATGGAAC
* * *
35537 ACAAGGATGATAAATTGTAACGTTATTTTATCAGATCAAATTTCAATCTTCTATTTTCAGAACAA
131 ACAAGGATCATAAATTGTAACGGTATTTT-TCGGATCAAA-TTCAATCTTCTATTTTCAGAACAA
*
35602 AAAATGAATTTTAAGAAGAGAAAAATGACCTTTGAGAATAGCAACGACTCGATTGCAGAGAGATT
194 AAAATGAATTCTAAGAAGAGAAAAATGACCTTTGAGAATAGCAACGACTCGATTGCAGAGAGATT
* * *
35667 CGTCGTTCT-TGGTC-T-GAT-CATTGTTCCCTTCCTCTTTCTCTTCTTCCTCATTTTGAACTCC
259 CATCGTTCTCTGGTCATAGATCCATTGTTCCCTTCCTCTTTCTCTTCTTCCTCAGTTTCAACTCC
*
35728 ACTGATGATATGAAAATTAAATCAGACAT-AAAGGGGGAAAACTGAAATAATTGAAATTGAATTA
324 ACTGATGATATGAAAATTAAATCAGACATGAAAGGGGGAAAACTGAAATAATTGAAATTGAAATA
35792 GGAAATAAAA
389 GGAAATAAAA
*
35802 TACCTCCAATGCTCATGAATTCTCTGTTGACACACTGCCTTAGTGCCTGTGATACGGAGGCCATG
1 TACCTCCAATGCTCAAGAATTCTCTGTTGACACACTGCCTTAGTGCCTGTGATACGGAGGCCATG
*
35867 GTTTCTCAAATAAGCTTTGAGTTCTTTCATGCTTAAGCTTTCTAAGTCACCTCCTTCTATGGAAC
66 GTTTCTCAAATAAGCTTTGAGTTCTTTCAAGCTTAAGCTTTCTAAGTCACCTCCTTCTATGGAAC
*
35932 ACAAGGATGATAAATTGTAACGGTATTTTATCGGATCAAATTCAATCTTCTATTTTCAGAACAAA
131 ACAAGGATCATAAATTGTAACGGTATTTT-TCGGATCAAATTCAATCTTCTATTTTCAGAACAAA
* *
35997 AAATGAATTTTAAGAAGAGAAAAATGACCTTTGACAATAGCAACGACTCGATTGCAGAGAGATTC
195 AAATGAATTCTAAGAAGAGAAAAATGACCTTTGAGAATAGCAACGACTCGATTGCAGAGAGATTC
* *
36062 GTCGTTCT-TGGTC-T-GAT-CATTGTTCCCTTCCTC-TTCTCTTCTTCCTCA-TTTGAACTCCA
260 ATCGTTCTCTGGTCATAGATCCATTGTTCCCTTCCTCTTTCTCTTCTTCCTCAGTTTCAACTCCA
*
36121 CTGATGATATGAAAATTAAATCAGACAT-AAAGGGGGAAAACTGAAATAATTGAAATTGAATTAG
325 CTGATGATATGAAAATTAAATCAGACATGAAAGGGGGAAAACTGAAATAATTGAAATTGAAATAG
36185 GAAATAAAA
390 GAAATAAAA
*
36194 TACCTCCAATGCTCATGAATTCTCTGTTGACACACTGCCTTAGTGCCTGTGATACGGAGGCCATG
1 TACCTCCAATGCTCAAGAATTCTCTGTTGACACACTGCCTTAGTGCCTGTGATACGGAGGCCATG
* * * * * * *
36259 GTTTCTCAAATAAGCTTTGTGTTCTTTCAAGCTCATGCTTTCCAGGTCACCTCCTTCTGTGCAAC
66 GTTTCTCAAATAAGCTTTGAGTTCTTTCAAGCTTAAGCTTTCTAAGTCACCTCCTTCTATGGAAC
* * * * *
36324 ACAAGGATAAAAAATTGTAAGGCCGT-TTTTTCCGGATCAAATTCAATCTTCTAATTTCAAAACA
131 ACAAGGATCATAAATTGTAA--CGGTATTTTT-CGGATCAAATTCAATCTTCTATTTTCAGAACA
** * * *
36388 AAAAACTGAATTCTAAGAAGAG-AATTTG-CCTTTGAGAATAGCAATGACCCGATTGCAAAGAGA
193 AAAAA-TGAATTCTAAGAAGAGAAAAATGACCTTTGAGAATAGCAACGACTCGATTGCAGAGAGA
*** * * *
36451 TTCATCGTCCTCAATCCCATCATTATAGTCCGAATTGCTCCCTTTGTCTTCCTCTTTCTGTTCTT
257 TTCATCGT--TC--TCTGGTCA-TAGA-TCC--ATTG-TTCC-----CTTCCTCTTTCTCTTCTT
** * * * * * * * *
36516 CCTCAGTTTCTTCTCTACCGATGATATGAAAATAAAATCAAACTTAAAAGGGGAAAAACT-AATT
308 CCTCAGTTTCAACTCCACTGATGATATGAAAATTAAATCAGACATGAAAGGGGGAAAACTGAAAT
* * * *
36580 AGTGGAAATTGAAATAGGAACTTAAA
373 AATTGAAATTGAAATAGGAAATAAAA
*
36606 TACCTCCAATGCTCAAGAATTCTCTGTATG-CACACTGCCTTGGTGCCTGTGATACGGAGGCCAT
1 TACCTCCAATGCTCAAGAATTCTCTGT-TGACACACTGCCTTAGTGCCTGTGATACGGAGGCCAT
* * * * *
36670 GGTTTCTCAAATAAGTTTTGAGTTCTTTCAGGCTTAAGCTTTCTAAGTCTCCACCTTCTATGGAG
65 GGTTTCTCAAATAAGCTTTGAGTTCTTTCAAGCTTAAGCTTTCTAAGTCACCTCCTTCTATGGAA
* * * *** * * *
36735 CACAAGGATCAGAAA----AAAGGCATTTTTTTAATCAAAATCAATCTTCTATTTTTAGAAGAAA
130 CACAAGGATCATAAATTGTAACGGTATTTTTCGGATCAAATTCAATCTTCTATTTTCAGAACAAA
**
36796 AAACTGAATTCTAAGAAGAGAACGATGACCTTTGAGA
195 AAA-TGAATTCTAAGAAGAGAAAAATGACCTTTGAGA
36833 TGGAAATGAT
Statistics
Matches: 1263, Mismatches: 126, Indels: 73
0.86 0.09 0.05
Matches are distributed among these distances:
392 263 0.21
393 58 0.05
394 149 0.12
395 186 0.15
396 4 0.00
397 56 0.04
398 6 0.00
399 5 0.00
400 2 0.00
401 1 0.00
402 1 0.00
404 8 0.01
405 3 0.00
406 52 0.04
407 152 0.12
408 30 0.02
409 71 0.06
410 7 0.01
411 14 0.01
412 180 0.14
413 15 0.01
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32
Consensus pattern (398 bp):
TACCTCCAATGCTCAAGAATTCTCTGTTGACACACTGCCTTAGTGCCTGTGATACGGAGGCCATG
GTTTCTCAAATAAGCTTTGAGTTCTTTCAAGCTTAAGCTTTCTAAGTCACCTCCTTCTATGGAAC
ACAAGGATCATAAATTGTAACGGTATTTTTCGGATCAAATTCAATCTTCTATTTTCAGAACAAAA
AATGAATTCTAAGAAGAGAAAAATGACCTTTGAGAATAGCAACGACTCGATTGCAGAGAGATTCA
TCGTTCTCTGGTCATAGATCCATTGTTCCCTTCCTCTTTCTCTTCTTCCTCAGTTTCAACTCCAC
TGATGATATGAAAATTAAATCAGACATGAAAGGGGGAAAACTGAAATAATTGAAATTGAAATAGG
AAATAAAA
Found at i:36714 original size:804 final size:791
Alignment explanation
Indices: 35000--36830 Score: 2176
Period size: 804 Copynumber: 2.3 Consensus size: 791
34990 ATGATGAAAT
* *
35000 TACCTCCAATGCTCAAGAATTCTTTGTTGGCACACTGCCTTAGTGCCTGTGATAAGGAGGCCATG
1 TACCTCCAATGCTCAAGAATTCTCTGTT-GCACACTGCCTTAGTGCCTGTGATACGGAGGCCATG
* * * *
35065 ATTTCTCAAATAAGCTTTCAGTTCTTTCAAGCTTAAGCTTTCAAAGTCACCCCCTTCTATGGAAC
65 GTTTCTCAAATAAGCTTTGAGTTCTTTCAAGCTTAAGCTTTCTAAGTCACCACCTTCTATGGAAC
* * * * *
35130 A-ACAGAAACATATATTGTAAGGGCATTTTTTGGGATCAAATTCAATCTTCTATTTTCA-AACAA
130 ACA-AGGATCATAAATTGTAAAGGCA-TTTTTCGGATCAAATTCAATCTTCTATTTTCAGAACAA
* * * * *
35193 AAAATGAATTCTACGAAGAGAAAGATGACCTTTGAGAATTGCAATGACTTGATTGCAGAGAGAAT
193 AAAATGAATTCTAAGAAGAGAAAGATGACCTTTGACAATAGCAACGACTCGATTGCAGAGAGAAT
* *
35258 CATCGTTCTCAGTCCGGTCATTATAGTTCACATTGTTCCTTTCCTCTTCCTCTTCTTCCCCAGTT
258 CATCGTTCT-A-T-CGGTC---ATAGAT-ACATTGTTCCCTTCCTCTTCCTCTTCTTCCCCAGTT
* ** ****
35323 TCATCTCCACTGATGATATCAAAATTAATCAAAATTGGGGAGGGGGGGGGGGCAAAATAATTGAA
316 TCAACTCCACTGATGATATCAAAATTAATCAAAATT---GAAAGGGGGAAAACAAAATAATTGAA
* *
35388 ATAGAAATAGGAATGTAAATACCTCCAATGCTCAAGAATTCTCTGTTGACACATTGCCTTACTGC
378 ATAGAAATAGGAATGAAAATACCTCCAATGCTCAAGAATTCTCTGTTGACACACTGCCTTACTGC
* * *
35453 CTGTGATACGAAGGCCATGATTTCTCAAATAAGCTTTGAGTTCTTTCATGCTTAAGCTTTCTAAG
443 CTGTGATACGAAGGCCATGATTTCTCAAATAAGCTTTGAGTTCTTTCAAGCTCAAGCTTTCCAAG
* * * *
35518 TCACCTCCTTCTATGGAACACAAGGATGATAAATTGTAACGTTATTTTATCAGATCAAATTTCAA
508 TCACCTCCTTCTATGCAACACAAGGATAAAAAATTGTAACGTTATTTTACCAGATCAAATTTCAA
* * *
35583 TCTTCTATTTTCAGAACAAAAAATGAATTTTAAGAAGAGAAAAATGACCTTTGAGAATAGCAACG
573 TCTTCTAATTTCAAAACAAAAAATGAATTCTAAGAAGAGAAAAATGACCTTTGAGAATAGCAACG
* * * *** *
35648 ACTCGATTGCAGAGAGATTCGTCGTTCTTGGTCTGATCATTGTTCCCTTCCTCTTTCTCTTCTTC
638 ACCCGATTGCAAAGAGATTCATCGTTCTCCATCTGATCATTGTCCCCTTCCTCTTTCTCTTCTTC
* * * * * *
35713 CTCATTTTGAACTCCACTGATGATATGAAAATTAAATCAGACATAAAGGGGGAAAACTGAAATAA
703 CTCAGTTTCAACTCCACCGATGATATGAAAATAAAATCAAACATAAAGGGGAAAAACTGAAATAA
* *
35778 TTGAAATTGAATTAGGAAATAAAA
768 TGGAAATTGAAATAGGAAATAAAA
*
35802 TACCTCCAATGCTCATGAATTCTCTGTTGACACACTGCCTTAGTGCCTGTGATACGGAGGCCATG
1 TACCTCCAATGCTCAAGAATTCTCTGTTG-CACACTGCCTTAGTGCCTGTGATACGGAGGCCATG
* *
35867 GTTTCTCAAATAAGCTTTGAGTTCTTTCATGCTTAAGCTTTCTAAGTCACCTCCTTCTATGGAAC
65 GTTTCTCAAATAAGCTTTGAGTTCTTTCAAGCTTAAGCTTTCTAAGTCACCACCTTCTATGGAAC
* * *
35932 ACAAGGATGATAAATTGTAACGGTATTTTATCGGATCAAATTCAATCTTCTATTTTCAGAACAAA
130 ACAAGGATCATAAATTGTAAAGGCATTTT-TCGGATCAAATTCAATCTTCTATTTTCAGAACAAA
* * *
35997 AAATGAATTTTAAGAAGAGAAAAATGACCTTTGACAATAGCAACGACTCGATTGCAGAGAGATTC
194 AAATGAATTCTAAGAAGAGAAAGATGACCTTTGACAATAGCAACGACTCGATTGCAGAGAGAATC
* * *
36062 GTCGTTCT-T-GGTC-T-GAT-CATTGTTCCCTTCCTCTT-CTCTTCTTCCTCA-TTTGAACTCC
259 ATCGTTCTATCGGTCATAGATACATTGTTCCCTTCCTCTTCCTCTTCTTCCCCAGTTTCAACTCC
* * * * *
36120 ACTGATGATATGAAAATTAAATCAGACA-T-AAAGGGGGAAAACTGAAATAATTGAAATTGAATT
324 ACTGATGATATCAAAATT-AATCA-AAATTGAAAGGGGGAAAAC-AAAATAATTGAAATAGAAAT
* *
36183 AGGAAAT-AAAATACCTCCAATGCTCATGAATTCTCTGTTGACACACTGCCTTAGTGCCTGTGAT
386 AGG-AATGAAAATACCTCCAATGCTCAAGAATTCTCTGTTGACACACTGCCTTACTGCCTGTGAT
* * * * *
36247 ACGGAGGCCATGGTTTCTCAAATAAGCTTTGTGTTCTTTCAAGCTCATGCTTTCCAGGTCACCTC
450 ACGAAGGCCATGATTTCTCAAATAAGCTTTGAGTTCTTTCAAGCTCAAGCTTTCCAAGTCACCTC
* *
36312 CTTCTGTGCAACACAAGGATAAAAAATTGTAAGGCCGTT-TTTT-CCGGATCAAA-TTCAATCTT
515 CTTCTATGCAACACAAGGATAAAAAATTGTAA---CGTTATTTTACCAGATCAAATTTCAATCTT
** *
36374 CTAATTTCAAAACAAAAAACTGAATTCTAAGAAGAG-AATTTG-CCTTTGAGAATAGCAATGACC
577 CTAATTTCAAAACAAAAAA-TGAATTCTAAGAAGAGAAAAATGACCTTTGAGAATAGCAACGACC
*
36437 CGATTGCAAAGAGATTCATCGTCCTCAATCCCATCATTATAGTCCGAATTGCTCCCTTTGTCTTC
641 CGATTGCAAAGAGATTCATCGT--TC--T-CCATC--T-GA-T-C--ATTG-TCCC-----CTTC
* ** * *
36502 CTCTTTCTGTTCTTCCTCAGTTTCTTCTCTACCGATGATATGAAAATAAAATCAAACTTAAAAGG
688 CTCTTTCTCTTCTTCCTCAGTTTCAACTCCACCGATGATATGAAAATAAAATCAAACAT-AAAGG
* * * *
36567 GGAAAAACT-AATTAGTGGAAATTGAAATAGGAACTTAAA
752 GGAAAAACTGAAATAATGGAAATTGAAATAGGAAATAAAA
*
36606 TACCTCCAATGCTCAAGAATTCTCTGTATGCACACTGCCTTGGTGCCTGTGATACGGAGGCCATG
1 TACCTCCAATGCTCAAGAATTCTCTGT-TGCACACTGCCTTAGTGCCTGTGATACGGAGGCCATG
* * * *
36671 GTTTCTCAAATAAGTTTTGAGTTCTTTCAGGCTTAAGCTTTCTAAGTCTCCACCTTCTATGGAGC
65 GTTTCTCAAATAAGCTTTGAGTTCTTTCAAGCTTAAGCTTTCTAAGTCACCACCTTCTATGGAAC
* *** * * *
36736 ACAAGGATCAGAAA----AAAGGCATTTTTTTAATCAAAATCAATCTTCTATTTTTAGAAGAAAA
130 ACAAGGATCATAAATTGTAAAGGCATTTTTCGGATCAAATTCAATCTTCTATTTTCAGAACAAAA
*
36797 AACTGAATTCTAAGAAGAGAACGATGACCTTTGA
195 AA-TGAATTCTAAGAAGAGAAAGATGACCTTTGA
36831 GATGGAAATG
Statistics
Matches: 887, Mismatches: 109, Indels: 68
0.83 0.10 0.06
Matches are distributed among these distances:
786 46 0.05
787 188 0.21
788 28 0.03
789 29 0.03
790 23 0.03
791 21 0.02
793 3 0.00
794 2 0.00
795 1 0.00
796 1 0.00
798 8 0.01
799 35 0.04
800 38 0.04
801 5 0.01
802 164 0.18
803 71 0.08
804 209 0.24
805 15 0.02
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32
Consensus pattern (791 bp):
TACCTCCAATGCTCAAGAATTCTCTGTTGCACACTGCCTTAGTGCCTGTGATACGGAGGCCATGG
TTTCTCAAATAAGCTTTGAGTTCTTTCAAGCTTAAGCTTTCTAAGTCACCACCTTCTATGGAACA
CAAGGATCATAAATTGTAAAGGCATTTTTCGGATCAAATTCAATCTTCTATTTTCAGAACAAAAA
ATGAATTCTAAGAAGAGAAAGATGACCTTTGACAATAGCAACGACTCGATTGCAGAGAGAATCAT
CGTTCTATCGGTCATAGATACATTGTTCCCTTCCTCTTCCTCTTCTTCCCCAGTTTCAACTCCAC
TGATGATATCAAAATTAATCAAAATTGAAAGGGGGAAAACAAAATAATTGAAATAGAAATAGGAA
TGAAAATACCTCCAATGCTCAAGAATTCTCTGTTGACACACTGCCTTACTGCCTGTGATACGAAG
GCCATGATTTCTCAAATAAGCTTTGAGTTCTTTCAAGCTCAAGCTTTCCAAGTCACCTCCTTCTA
TGCAACACAAGGATAAAAAATTGTAACGTTATTTTACCAGATCAAATTTCAATCTTCTAATTTCA
AAACAAAAAATGAATTCTAAGAAGAGAAAAATGACCTTTGAGAATAGCAACGACCCGATTGCAAA
GAGATTCATCGTTCTCCATCTGATCATTGTCCCCTTCCTCTTTCTCTTCTTCCTCAGTTTCAACT
CCACCGATGATATGAAAATAAAATCAAACATAAAGGGGAAAAACTGAAATAATGGAAATTGAAAT
AGGAAATAAAA
Found at i:37088 original size:259 final size:257
Alignment explanation
Indices: 36611--37091 Score: 614
Period size: 259 Copynumber: 1.9 Consensus size: 257
36601 TTAAATACCT
*
36611 CCAATGCTCAAGAATTCTCTGTATGCACACTGCCTTGGTGCCTGTGATACGGAGGCCATGGTTTC
1 CCAATGCTCAAGAATTCTCTGTATGCACACTGCCTTAGTGCCTGTGATACGGAGGCCATGGTTTC
* * * * * *
36676 TCAAATAAGTTTTGAGTTCTTTCAGGCTTAAGCTTTCTAAGTCTCCACCTTCTATGGAGCACAAG
66 TCAAATAAGCTTTGAGTTCTTTCAAGCTCAAGCTGTCTAAG-CTCCACCTCCTATGGAACACAAG
* * * * * *
36741 GATCAGAAAAAAGGCATTTTTTTAATCAAAATCAATCTTCTATTTTTAGAAGAAAAAACTGAATT
130 GATCAGAAAAAAGGCATTTTTTGAAGCAAAATCAATCTTCTATTTTCAAAACAAAAAAC-GAACT
* * * *
36806 CTAAGAAGAGAACGATGACCTTTGAGATGGAAATGATTCGATTGCTGACAGATTCGTCGCTCTC
194 CCAAGAACAGAACAAAGACCTTTGAGATGGAAATGATTCGATTGCTGACAGATTCGTCGCTCTC
*
36870 CCAATGTTCAAGAATTCTCTGT-TGACACACTGCCTTAGTGCCTGTGATACGGAGGCCATGGTTT
1 CCAATGCTCAAGAATTCTCTGTATG-CACACTGCCTTAGTGCCTGTGATACGGAGGCCATGGTTT
36934 CTCAAATAAGCTTTGAGTTCTTTCAAGCTCAAGCTGTCTAAG-T-CACCTCCTATGGAACACAAG
65 CTCAAATAAGCTTTGAGTTCTTTCAAGCTCAAGCTGTCTAAGCTCCACCTCCTATGGAACACAAG
* * * * *
36997 GATCA-ATAATTGTATGGTCATTTTCTTGGAGCAGATTCAATCTTCTATTTTCAAAACAAAAAA-
130 GATCAGA-AA---AAAGG-CATTTT-TTGAAGCAAAATCAATCTTCTATTTTCAAAACAAAAAAC
*
37060 GAACTCCGAGAACAGAA-AAAGAACCTTTGAGA
189 GAACTCCAAGAACAGAACAAAG-ACCTTTGAGA
37092 ATATTAATGA
Statistics
Matches: 190, Mismatches: 24, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
255 1 0.01
256 25 0.13
257 1 0.01
258 4 0.02
259 123 0.65
260 6 0.03
261 30 0.16
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (257 bp):
CCAATGCTCAAGAATTCTCTGTATGCACACTGCCTTAGTGCCTGTGATACGGAGGCCATGGTTTC
TCAAATAAGCTTTGAGTTCTTTCAAGCTCAAGCTGTCTAAGCTCCACCTCCTATGGAACACAAGG
ATCAGAAAAAAGGCATTTTTTGAAGCAAAATCAATCTTCTATTTTCAAAACAAAAAACGAACTCC
AAGAACAGAACAAAGACCTTTGAGATGGAAATGATTCGATTGCTGACAGATTCGTCGCTCTC
Found at i:38218 original size:16 final size:16
Alignment explanation
Indices: 38189--38224 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
38179 TAATTAACCA
38189 AAAT-TATTAGATATT
1 AAATATATTAGATATT
*
38204 AAATATATTATATATT
1 AAATATATTAGATATT
38220 AAATA
1 AAATA
38225 CATATTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
AAATATATTAGATATT
Found at i:39926 original size:56 final size:56
Alignment explanation
Indices: 39840--39972 Score: 266
Period size: 56 Copynumber: 2.4 Consensus size: 56
39830 ACGCAAGAAC
39840 ACTTTCCATCACAAATTATAGCGCCCTGCTTCTTCCTTCCCCCTCTCCCAGTTCTT
1 ACTTTCCATCACAAATTATAGCGCCCTGCTTCTTCCTTCCCCCTCTCCCAGTTCTT
39896 ACTTTCCATCACAAATTATAGCGCCCTGCTTCTTCCTTCCCCCTCTCCCAGTTCTT
1 ACTTTCCATCACAAATTATAGCGCCCTGCTTCTTCCTTCCCCCTCTCCCAGTTCTT
39952 ACTTTCCATCACAAATTATAG
1 ACTTTCCATCACAAATTATAG
39973 AACACAGAAG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 77 1.00
ACGTcount: A:0.20, C:0.38, G:0.07, T:0.35
Consensus pattern (56 bp):
ACTTTCCATCACAAATTATAGCGCCCTGCTTCTTCCTTCCCCCTCTCCCAGTTCTT
Found at i:40071 original size:2 final size:2
Alignment explanation
Indices: 40066--40129 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
40056 AACCAGTTAG
40066 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
40108 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
40130 TGAACAAATT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43442 original size:22 final size:23
Alignment explanation
Indices: 43412--43463 Score: 81
Period size: 22 Copynumber: 2.3 Consensus size: 23
43402 AGCTCGTACC
43412 GAATCGCGATTTTGAAACGACTA
1 GAATCGCGATTTTGAAACGACTA
*
43435 GAAT-GCGATTTTGAAGCGACTA
1 GAATCGCGATTTTGAAACGACTA
43457 GAA-CGCG
1 GAATCGCG
43464 TTTGTACTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 23 0.85
23 4 0.15
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.23
Consensus pattern (23 bp):
GAATCGCGATTTTGAAACGACTA
Found at i:47824 original size:6 final size:6
Alignment explanation
Indices: 47813--47843 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
47803 AAATAACTCC
47813 TTATAA TTATAA TTATAA TTATAA TTATAA T
1 TTATAA TTATAA TTATAA TTATAA TTATAA T
47844 GTTTTATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTATAA
Found at i:48430 original size:33 final size:33
Alignment explanation
Indices: 48385--48447 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
48375 GGCGACATCG
*
48385 AAGGTCTCCTGCAACAGACGTGGTGGATGCTCC
1 AAGGTCTCCTGCAACAGACGCGGTGGATGCTCC
* * *
48418 AAGGTCTGCTGCATCAGATGCGGTGGATGC
1 AAGGTCTCCTGCAACAGACGCGGTGGATGC
48448 ATCCTCTGCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.21, C:0.24, G:0.33, T:0.22
Consensus pattern (33 bp):
AAGGTCTCCTGCAACAGACGCGGTGGATGCTCC
Found at i:53363 original size:20 final size:20
Alignment explanation
Indices: 53338--53430 Score: 177
Period size: 20 Copynumber: 4.7 Consensus size: 20
53328 TTTTCCTAAT
53338 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
53358 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
53378 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
53398 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
53418 TCGCAACGCGAAT
1 TCGCAATGCGAAT
53431 CTGACTATCG
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
20 72 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:53440 original size:20 final size:20
Alignment explanation
Indices: 53417--53463 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
53407 GAATACGTAA
*
53417 ATCGCAACGCGAATCTGACT
1 ATCGCAACGAGAATCTGACT
*
53437 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGAATCTGACT
53457 ATCGCAA
1 ATCGCAA
53464 TATTGAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAACGAGAATCTGACT
Found at i:53441 original size:60 final size:61
Alignment explanation
Indices: 53297--53443 Score: 183
Period size: 60 Copynumber: 2.4 Consensus size: 61
53287 GTTTCCAGAT
* * * * *
53297 TCGCAACGCGATTCTGACTATCGCATTGCGATTTTCCTAATTCGCAATGCGAATACGTAAA
1 TCGCAACGCGAATCTGACTATCGCAATGCGATATACCTAAATCGCAATGCGAATACGTAAA
* * *
53358 TCGCAATGCGAATAC-GTA-AATCGCAATGCGA-ATACGTAAATCGCAATGCGAATACGTAAA
1 TCGCAACGCGAAT-CTG-ACTATCGCAATGCGATATACCTAAATCGCAATGCGAATACGTAAA
53418 TCGCAACGCGAATCTGACTATCGCAA
1 TCGCAACGCGAATCTGACTATCGCAA
53444 CGAGATTCTG
Statistics
Matches: 72, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
59 2 0.03
60 45 0.62
61 23 0.32
62 2 0.03
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (61 bp):
TCGCAACGCGAATCTGACTATCGCAATGCGATATACCTAAATCGCAATGCGAATACGTAAA
Found at i:53461 original size:60 final size:60
Alignment explanation
Indices: 53297--53464 Score: 141
Period size: 60 Copynumber: 2.8 Consensus size: 60
53287 GTTTCCAGAT
* ** * **
53297 TCGCAACGCGATTCTGACTATCGCATTGCGATT-TTCCTAATTCGCAATGCGAATACGTAAA
1 TCGCAACGCGAATCTGACTATCGCAACGAGATTCTGACT-A-TCGCAATGCGAATACGTAAA
* * * *
53358 TCGCAATGCGAATAC-GTA-AATCGCAATGCGA-ATAC-GTA-AATCGCAATGCGAATACGTAAA
1 TCGCAACGCGAAT-CTG-ACTATCGCAA--CGAGATTCTG-ACTATCGCAATGCGAATACGTAAA
53418 TCGCAACGCGAATCTGACTATCGCAACGAGATTCTGACTATCGCAAT
1 TCGCAACGCGAATCTGACTATCGCAACGAGATTCTGACTATCGCAAT
53465 ATTGAATTTC
Statistics
Matches: 82, Mismatches: 14, Indels: 23
0.69 0.12 0.19
Matches are distributed among these distances:
58 3 0.04
59 6 0.07
60 49 0.60
61 19 0.23
62 4 0.05
63 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (60 bp):
TCGCAACGCGAATCTGACTATCGCAACGAGATTCTGACTATCGCAATGCGAATACGTAAA
Found at i:54356 original size:24 final size:24
Alignment explanation
Indices: 54291--54358 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
54281 GTGAGTACTA
*
54291 GTCAATATTCGAAATTTGATCTTG
1 GTCAATACTCGAAATTTGATCTTG
* *
54315 GTCAATACCCGAACTTTGATCTTG
1 GTCAATACTCGAAATTTGATCTTG
* *
54339 GTCAATACTCGGATTTTGAT
1 GTCAATACTCGAAATTTGAT
54359 GATTTTTCAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (24 bp):
GTCAATACTCGAAATTTGATCTTG
Found at i:56786 original size:34 final size:34
Alignment explanation
Indices: 56743--56875 Score: 128
Period size: 33 Copynumber: 3.8 Consensus size: 34
56733 GACATTCATT
56743 TGACTATCGCAACGCAGA-AATCGCAACGCGAATA
1 TGACTATCGCAACG-AGAGAATCGCAACGCGAATA
*
56777 TGACTATCGCAACACGGAAATGACTATCGCAACGCTGAAT-
1 TGACTATCGC-A-AC-GAGA-GA--ATCGCAACGC-GAATA
*
56817 TGACTATCGCAACGAGAGAATCGCAATGCGAA-A
1 TGACTATCGCAACGAGAGAATCGCAACGCGAATA
** *
56850 TGAAAATCACAACGAGAGAATCGCAA
1 TGACTATCGCAACGAGAGAATCGCAA
56876 TGCAAAAATG
Statistics
Matches: 84, Mismatches: 6, Indels: 19
0.77 0.06 0.17
Matches are distributed among these distances:
33 26 0.31
34 19 0.23
35 1 0.01
36 6 0.07
37 4 0.05
38 3 0.04
39 1 0.01
40 20 0.24
41 4 0.05
ACGTcount: A:0.40, C:0.23, G:0.21, T:0.16
Consensus pattern (34 bp):
TGACTATCGCAACGAGAGAATCGCAACGCGAATA
Found at i:56787 original size:20 final size:21
Alignment explanation
Indices: 56762--56830 Score: 99
Period size: 20 Copynumber: 3.4 Consensus size: 21
56752 CAACGCAGAA
56762 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAATATGACT
*
56782 ATCGCAACACGGAA-ATGACT
1 ATCGCAACGCGGAATATGACT
*
56802 ATCGCAACGCTGAAT-TGACT
1 ATCGCAACGCGGAATATGACT
56822 ATCGCAACG
1 ATCGCAACG
56831 AGAGAATCGC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
20 41 0.93
21 3 0.07
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCGGAATATGACT
Found at i:56865 original size:33 final size:34
Alignment explanation
Indices: 56826--56897 Score: 119
Period size: 33 Copynumber: 2.1 Consensus size: 34
56816 TTGACTATCG
*
56826 CAACGAGAGAATCGCAATGC-GAAATGAAAATCA
1 CAACGAGAGAATCGCAATGCAAAAATGAAAATCA
*
56859 CAACGAGAGAATCGCAATGCAAAAATGAAAATCG
1 CAACGAGAGAATCGCAATGCAAAAATGAAAATCA
56893 CAACG
1 CAACG
56898 CGAATTTAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 20 0.56
34 16 0.44
ACGTcount: A:0.49, C:0.19, G:0.21, T:0.11
Consensus pattern (34 bp):
CAACGAGAGAATCGCAATGCAAAAATGAAAATCA
Found at i:56973 original size:33 final size:34
Alignment explanation
Indices: 56912--57007 Score: 124
Period size: 33 Copynumber: 2.8 Consensus size: 34
56902 TTTAGTTTCG
*
56912 CGTTGCGATTTTCATTTTTGCATTGCGATTCTC-A
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCTA
56946 CGTTGCGATTTTCATTTCGCATTGCGATTCTCTA
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCTA
** *
56980 -GTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
57008 AGTCTGTTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
33 31 0.55
34 25 0.45
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.43
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCTA
Found at i:57132 original size:14 final size:14
Alignment explanation
Indices: 57113--57149 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
57103 CATCAATTAA
57113 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
57127 ACAAATCATCTTTT
1 ACAAATCAACATTT
57141 ACAAATCAA
1 ACAAATCAA
57150 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:59059 original size:103 final size:103
Alignment explanation
Indices: 58875--59203 Score: 561
Period size: 103 Copynumber: 3.2 Consensus size: 103
58865 CCATATAATA
* *
58875 ATGT-CCATAAGGACCACATATCATTCCTTAATAATCATATACATATGCCAAGGATCAAGTATGT
1 ATGTCCCA-AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGT
* *
58939 GTCTCACCAGACTTCACACACGTTCCAAAGAATACATAT
65 GTCTCACCAGACCTCACACATGTTCCAAAGAATACATAT
58978 ATGTCCCAAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTG
1 ATGTCCCAAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTG
*
59043 TCTCACCAGACCTCACACATATTCCAAAGAATACATAT
66 TCTCACCAGACCTCACACATGTTCCAAAGAATACATAT
* *
59081 ATGTCCCGAATGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTG
1 ATGTCCCAAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTG
59146 TCTCACCAGACCTCACACATGTTCCAAAGAATACATAT
66 TCTCACCAGACCTCACACATGTTCCAAAGAATACATAT
* *
59184 ATGTCCCGAATGACCACATA
1 ATGTCCCAAAGGACCACATA
59204 GAGCCTCTAC
Statistics
Matches: 217, Mismatches: 8, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
103 214 0.99
104 3 0.01
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.26
Consensus pattern (103 bp):
ATGTCCCAAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTG
TCTCACCAGACCTCACACATGTTCCAAAGAATACATAT
Found at i:66255 original size:20 final size:22
Alignment explanation
Indices: 66230--66269 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
66220 AGTCGTATAT
66230 AGCCG-TTGGGGATG-TTTTAG
1 AGCCGTTTGGGGATGATTTTAG
66250 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
66270 TATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.15, C:0.10, G:0.38, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTAG
Found at i:66324 original size:21 final size:22
Alignment explanation
Indices: 66298--66340 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
66288 CCAGAATGGG
66298 GGGAATCGATA-CCCCTTCATA
1 GGGAATCGATACCCCCTTCATA
66319 GGGAATCGATACCCCCTTCATA
1 GGGAATCGATACCCCCTTCATA
66341 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (22 bp):
GGGAATCGATACCCCCTTCATA
Found at i:66406 original size:21 final size:21
Alignment explanation
Indices: 66380--66419 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
66370 TGAACAGGGG
66380 GGGAATCGGTACCCCCTGGGC
1 GGGAATCGGTACCCCCTGGGC
66401 GGGAATCGGTACCCCCTGG
1 GGGAATCGGTACCCCCTGG
66420 ACATTCTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.15, C:0.33, G:0.38, T:0.15
Consensus pattern (21 bp):
GGGAATCGGTACCCCCTGGGC
Found at i:66470 original size:20 final size:20
Alignment explanation
Indices: 66445--66523 Score: 78
Period size: 20 Copynumber: 4.2 Consensus size: 20
66435 GCTTTAGACA
*
66445 GGGGGGAATCAGTACCCCCT
1 GGGGGGAATCTGTACCCCCT
*
66465 GGGGGGGTATCTGTA--CCC-
1 -GGGGGGAATCTGTACCCCCT
*
66483 --GGGGTATCTGTACCCCCT
1 GGGGGGAATCTGTACCCCCT
*
66501 AGGGGGAATCTGTACCCCCT
1 GGGGGGAATCTGTACCCCCT
66521 GGG
1 GGG
66524 CAATCTTGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
19 3 0.06
20 19 0.39
21 12 0.24
ACGTcount: A:0.15, C:0.28, G:0.37, T:0.20
Consensus pattern (20 bp):
GGGGGGAATCTGTACCCCCT
Found at i:66488 original size:15 final size:15
Alignment explanation
Indices: 66468--66497 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
66458 ACCCCCTGGG
66468 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
66483 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
66498 CCTAGGGGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:66513 original size:35 final size:36
Alignment explanation
Indices: 66447--66517 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
66437 TTTAGACAGG
* *
66447 GGGGAATCAGTACCCCCTGGGGGGGTATCTGTACCC
1 GGGGAATCAGTACCCCCTGAGGGGGAATCTGTACCC
* *
66483 GGGGTATCTGTACCCCCT-AGGGGGAATCTGTACCC
1 GGGGAATCAGTACCCCCTGAGGGGGAATCTGTACCC
66518 CCTGGGCAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 15 0.48
36 16 0.52
ACGTcount: A:0.17, C:0.28, G:0.34, T:0.21
Consensus pattern (36 bp):
GGGGAATCAGTACCCCCTGAGGGGGAATCTGTACCC
Found at i:67962 original size:19 final size:20
Alignment explanation
Indices: 67919--67966 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
67909 TCTAAATCCT
*
67919 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
67939 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
67958 TTTTCAAAA
1 TTTTCAAAA
67967 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:68878 original size:34 final size:32
Alignment explanation
Indices: 68825--68894 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
68815 ACCTTACAAC
*
68825 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
68857 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
68891 TCCC
1 TCCC
68895 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:69139 original size:21 final size:21
Alignment explanation
Indices: 69109--69148 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
69099 AGTCGTATAT
69109 AGCCGTTGGGGATG-TTTTAG
1 AGCCGTTGGGGATGATTTTAG
69129 AGCCGCTTGGGGATGATTTT
1 AGCCG-TTGGGGATGATTTT
69149 TATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.15, C:0.12, G:0.38, T:0.35
Consensus pattern (21 bp):
AGCCGTTGGGGATGATTTTAG
Found at i:69326 original size:21 final size:21
Alignment explanation
Indices: 69301--69379 Score: 89
Period size: 21 Copynumber: 4.0 Consensus size: 21
69291 GCTTTAGACA
*
69301 GGGGGAATCAGTACCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
*
69322 GGGGGTATCTGTA--CCC---
1 GGGGGAATCTGTACCCCCTGG
*
69338 -GGGGTATCTGTACCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
69358 GGGGGAATCTGTACCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
69379 G
1 G
69380 CAATCTTGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
19 3 0.06
21 31 0.63
ACGTcount: A:0.14, C:0.28, G:0.38, T:0.20
Consensus pattern (21 bp):
GGGGGAATCTGTACCCCCTGG
Found at i:69343 original size:15 final size:15
Alignment explanation
Indices: 69323--69352 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
69313 ACCCCCTGGG
69323 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
69338 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
69353 CCTGGGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:69358 original size:36 final size:36
Alignment explanation
Indices: 69302--69373 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
69292 CTTTAGACAG
*
69302 GGGGAATCAGTACCCCCTGGGGGGGTATCTGTACCC
1 GGGGAATCAGTACCCCCTGGGGGGGAATCTGTACCC
* *
69338 GGGGTATCTGTACCCCCTGGGGGGGAATCTGTACCC
1 GGGGAATCAGTACCCCCTGGGGGGGAATCTGTACCC
69374 CCTGGGCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.15, C:0.28, G:0.36, T:0.21
Consensus pattern (36 bp):
GGGGAATCAGTACCCCCTGGGGGGGAATCTGTACCC
Found at i:70017 original size:103 final size:103
Alignment explanation
Indices: 69841--70161 Score: 579
Period size: 103 Copynumber: 3.1 Consensus size: 103
69831 TAATGTCCAT
*
69841 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
69906 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
69944 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
70009 GACCTCACACATGTTCCAAAGAATACATATATGTCTCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
* * *
70047 AATGACCACATATAATTCCTTAAGAATCATATGCATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
70112 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
*
70150 AAGAACCACATA
1 AAGGACCACATA
70162 GACCCTCTAC
Statistics
Matches: 209, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 209 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:71957 original size:42 final size:42
Alignment explanation
Indices: 71859--71957 Score: 110
Period size: 42 Copynumber: 2.4 Consensus size: 42
71849 TTGGAAGGGA
* * * *
71859 CCTCTTCAACGATGAAAGTGGCCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGAAAGGGGCCTCTTGAACGATGGGAGAGG
* ** *
71901 ACTCTTGAGGGATGATAGGGGCCTCTTGAACGATAGGG-GAGG
1 CCTCTTGAACGATGAAAGGGGCCTCTTGAACGAT-GGGAGAGG
71943 CCTCTTGAACGATGA
1 CCTCTTGAACGATGA
71958 CAGGTGAGTC
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
42 42 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.19, G:0.35, T:0.22
Consensus pattern (42 bp):
CCTCTTGAACGATGAAAGGGGCCTCTTGAACGATGGGAGAGG
Found at i:72475 original size:20 final size:20
Alignment explanation
Indices: 72452--72529 Score: 129
Period size: 20 Copynumber: 3.9 Consensus size: 20
72442 AATCGTAACA
*
72452 CGAAAATGACTACCGCAATG
1 CGAAAATGACTATCGCAATG
72472 CGAAAATGACTATCGCAATG
1 CGAAAATGACTATCGCAATG
72492 CGAAAATGACTATCGCAATG
1 CGAAAATGACTATCGCAATG
**
72512 CGAATTTGACTATCGCAA
1 CGAAAATGACTATCGCAA
72530 CGAGAGAATC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (20 bp):
CGAAAATGACTATCGCAATG
Found at i:72595 original size:53 final size:53
Alignment explanation
Indices: 72538--72656 Score: 143
Period size: 53 Copynumber: 2.2 Consensus size: 53
72528 AACGAGAGAA
* *
72538 TCGCAATGCGATTTTCA-TTTCGCATTGCGATTCTT-TCGTTGCGATAGTCATTT
1 TCGCATTGCGATTGTCATTTTCGCATTGCGATT-TTGTCGTTGCGATAGTCA-TT
* * * **
72591 TCGCATTGCGATAGTCATTTTCGCGTTGCGATTTTGTTGTTGCGATTTTCATT
1 TCGCATTGCGATTGTCATTTTCGCATTGCGATTTTGTCGTTGCGATAGTCATT
72644 TCGCATTGCGATT
1 TCGCATTGCGATT
72657 CTCTCGTTAC
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
53 30 0.54
54 26 0.46
ACGTcount: A:0.15, C:0.19, G:0.21, T:0.45
Consensus pattern (53 bp):
TCGCATTGCGATTGTCATTTTCGCATTGCGATTTTGTCGTTGCGATAGTCATT
Found at i:72601 original size:20 final size:20
Alignment explanation
Indices: 72576--72712 Score: 104
Period size: 20 Copynumber: 7.5 Consensus size: 20
72566 GATTCTTTCG
72576 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
72596 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
72616 TTGCGAT--T--TTGTT-G--
1 TTGCGATAGTCATT-TTCGCA
**
72630 TTGCGATTTTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
72649 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
* *
72663 TTACGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
*
72683 TTGCGATAATCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
72703 TTGCGATAGT
1 TTGCGATAGT
72713 AAACTATTCT
Statistics
Matches: 95, Mismatches: 8, Indels: 28
0.73 0.06 0.21
Matches are distributed among these distances:
14 13 0.14
16 12 0.13
17 6 0.06
18 5 0.05
19 7 0.07
20 52 0.55
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.43
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:72642 original size:87 final size:87
Alignment explanation
Indices: 72544--72709 Score: 287
Period size: 87 Copynumber: 1.9 Consensus size: 87
72534 AGAATCGCAA
* * *
72544 TGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATAGTCATTTTCGCATTGCGATAGTCAT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTACGATAGTCATTTTCGCATTGCGATAATCAT
*
72609 TTTCGCGTTGCGATTTTGTTGT
66 TTTCGCATTGCGATTTTGTTGT
*
72631 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTACGATAGTCATTTTCGCGTTGCGATAATCAT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTACGATAGTCATTTTCGCATTGCGATAATCAT
72696 TTTCGCATTGCGAT
66 TTTCGCATTGCGAT
72710 AGTAAACTAT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 74 1.00
ACGTcount: A:0.16, C:0.20, G:0.20, T:0.44
Consensus pattern (87 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTACGATAGTCATTTTCGCATTGCGATAATCAT
TTTCGCATTGCGATTTTGTTGT
Found at i:72676 original size:33 final size:34
Alignment explanation
Indices: 72599--72689 Score: 112
Period size: 33 Copynumber: 2.7 Consensus size: 34
72589 TTTCGCATTG
* * * *
72599 CGATAGTCATTTTCGCGTTGCGATTTTGTTGTTG
1 CGATAGTCATTTTCGCGTTGCGATTCTCTCGTTA
** *
72633 CGATTTTCA-TTTCGCATTGCGATTCTCTCGTTA
1 CGATAGTCATTTTCGCGTTGCGATTCTCTCGTTA
72666 CGATAGTCATTTTCGCGTTGCGAT
1 CGATAGTCATTTTCGCGTTGCGAT
72690 AATCATTTTC
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
33 26 0.57
34 20 0.43
ACGTcount: A:0.14, C:0.20, G:0.22, T:0.44
Consensus pattern (34 bp):
CGATAGTCATTTTCGCGTTGCGATTCTCTCGTTA
Found at i:74622 original size:20 final size:20
Alignment explanation
Indices: 74599--74687 Score: 99
Period size: 20 Copynumber: 4.5 Consensus size: 20
74589 TCTGAAACTT
74599 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
74619 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * **
74639 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
** *
74659 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
74678 AAAATCGCAA
1 AAAATCGCAA
74688 TGACAGAATC
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
19 11 0.18
20 49 0.82
ACGTcount: A:0.46, C:0.22, G:0.17, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:75088 original size:22 final size:22
Alignment explanation
Indices: 75026--75091 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
75016 TGACCGTGAA
* *
75026 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
*
75048 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
75070 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
75092 GGATGTCGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.21, C:0.15, G:0.39, T:0.24
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:75318 original size:20 final size:20
Alignment explanation
Indices: 75295--75340 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
75285 CAGATGCGCG
75295 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
75315 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
75335 TTGCGA
1 TTGCGA
75341 ATTAGGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.39
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:81363 original size:15 final size:15
Alignment explanation
Indices: 81343--81395 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 15
81333 AATTAAACTT
81343 ATAAAATTATAATGA
1 ATAAAATTATAATGA
* *
81358 ATAAAAATAAAGTATTG-
1 AT-AAAAT-TA-TAATGA
81375 ATAAAATTATAATGA
1 ATAAAATTATAATGA
81390 ATAAAA
1 ATAAAA
81396 ATAAAGTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
14 4 0.13
15 9 0.30
16 10 0.33
17 3 0.10
18 4 0.13
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.30
Consensus pattern (15 bp):
ATAAAATTATAATGA
Found at i:81379 original size:32 final size:32
Alignment explanation
Indices: 81343--81415 Score: 146
Period size: 32 Copynumber: 2.3 Consensus size: 32
81333 AATTAAACTT
81343 ATAAAATTATAATGAATAAAAATAAAGTATTG
1 ATAAAATTATAATGAATAAAAATAAAGTATTG
81375 ATAAAATTATAATGAATAAAAATAAAGTATTG
1 ATAAAATTATAATGAATAAAAATAAAGTATTG
81407 ATAAAATTA
1 ATAAAATTA
81416 AAAAGTAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (32 bp):
ATAAAATTATAATGAATAAAAATAAAGTATTG
Found at i:81380 original size:16 final size:16
Alignment explanation
Indices: 81361--81413 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
81351 ATAATGAATA
81361 AAAATAAAGTATTGAT
1 AAAATAAAGTATTGAT
* *
81377 AAAAT-TA-TAATGAAT
1 AAAATAAAGTATTG-AT
81392 AAAAATAAAGTATTGAT
1 -AAAATAAAGTATTGAT
81409 AAAAT
1 AAAAT
81414 TAAAAAGTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
14 4 0.14
15 3 0.10
16 15 0.52
17 3 0.10
18 4 0.14
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.30
Consensus pattern (16 bp):
AAAATAAAGTATTGAT
Found at i:81380 original size:17 final size:17
Alignment explanation
Indices: 81358--81417 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
81348 ATTATAATGA
81358 ATAAAAATAAAGTATTG
1 ATAAAAATAAAGTATTG
* *
81375 AT-AAAAT-TA-TAATG
1 ATAAAAATAAAGTATTG
81389 AATAAAAATAAAGTATTG
1 -ATAAAAATAAAGTATTG
*
81407 ATAAAATTAAA
1 ATAAAAATAAA
81418 AAGTAAATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
14 4 0.12
15 3 0.09
16 10 0.29
17 13 0.38
18 4 0.12
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.30
Consensus pattern (17 bp):
ATAAAAATAAAGTATTG
Found at i:82045 original size:23 final size:24
Alignment explanation
Indices: 81996--82081 Score: 66
Period size: 24 Copynumber: 3.5 Consensus size: 24
81986 TGAATGTGTT
* *
81996 CATGTTCGTTTATTTATTATTCTCGAA
1 CATGTTCGTTTA--TA-TGTTCACGAA
82023 CATGTTCGTTTA-ATGTTCACGAA
1 CATGTTCGTTTATATGTTCACGAA
* * * *
82046 TATATTTGTTTATATGTTCACAAA
1 CATGTTCGTTTATATGTTCACGAA
* *
82070 CGTGTTCATTTA
1 CATGTTCGTTTA
82082 GCATTCACAA
Statistics
Matches: 47, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
23 17 0.36
24 18 0.38
27 12 0.26
ACGTcount: A:0.26, C:0.14, G:0.13, T:0.48
Consensus pattern (24 bp):
CATGTTCGTTTATATGTTCACGAA
Found at i:87196 original size:18 final size:18
Alignment explanation
Indices: 87140--87196 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
87130 AACCAATAAT
*
87140 AATAAACATAAAATAATTG
1 AATAAA-ATAAAATAAATG
*
87159 GAT-AAA-AAAATGAAATTG
1 AATAAAATAAAAT-AAA-TG
87177 AATAAAATAAAATAAATG
1 AATAAAATAAAATAAATG
87195 AA
1 AA
87197 GATAAAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
16 5 0.16
17 3 0.10
18 10 0.32
19 8 0.26
20 5 0.16
ACGTcount: A:0.67, C:0.02, G:0.09, T:0.23
Consensus pattern (18 bp):
AATAAAATAAAATAAATG
Found at i:87308 original size:22 final size:20
Alignment explanation
Indices: 87276--87338 Score: 56
Period size: 22 Copynumber: 3.0 Consensus size: 20
87266 GCAAAGAAAC
*
87276 TAAAAATATAATGAAAATAAA
1 TAAATATATAAT-AAAATAAA
*
87297 TAAATAGTATAAATAAAATATA
1 TAAATA-TAT-AATAAAATAAA
*
87319 TATATATATAA-AAATATAAA
1 TAAATATATAATAAA-ATAAA
87339 AATGTATGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
19 3 0.09
20 6 0.17
21 8 0.23
22 15 0.43
23 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (20 bp):
TAAATATATAATAAAATAAA
Found at i:87324 original size:17 final size:17
Alignment explanation
Indices: 87278--87336 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
87268 AAAGAAACTA
87278 AAAATATA-ATGA-AAAT
1 AAAATATATAT-ATAAAT
*
87294 -AAATAAATAGTATAAAT
1 AAAATATATA-TATAAAT
*
87311 AAAATATATATATATAT
1 AAAATATATATATAAAT
87328 AAAA-ATATA
1 AAAATATATA
87337 AAAATGTATG
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
15 6 0.17
16 7 0.19
17 15 0.42
18 8 0.22
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (17 bp):
AAAATATATATATAAAT
Found at i:89058 original size:106 final size:106
Alignment explanation
Indices: 88874--90137 Score: 1960
Period size: 106 Copynumber: 12.0 Consensus size: 106
88864 GCATTGTTCC
* * * * * *
88874 GAGTCTAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTATTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * * *
88938 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
88980 GAGTCCAATATCCTTTGCCGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
89045 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
89086 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
89151 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
89192 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
89257 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGATGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
89298 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
89363 CCAGCGGTCCCTTCGTCTTGAAATTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
89404 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCAGAAATTGGGAAATTGTTTGTTAACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
89469 CCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
89510 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
89575 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
89616 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
89681 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
89722 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
89787 CTAGCGGTCCCTTCGTCATGAAGTTGAACTTGCATTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
89828 GAGTCCAATATCCTTCGC--T--A--TG-AA---G-T-TGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
89881 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
89922 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
89987 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
90028 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAATTTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
90093 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
90134 GAGT
1 GAGT
90138 GACACGATAT
Statistics
Matches: 1074, Mismatches: 71, Indels: 26
0.92 0.06 0.02
Matches are distributed among these distances:
94 81 0.08
95 1 0.00
96 2 0.00
98 1 0.00
99 2 0.00
100 4 0.00
101 2 0.00
102 1 0.00
104 2 0.00
105 1 0.00
106 977 0.91
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:89926 original size:94 final size:94
Alignment explanation
Indices: 89760--90062 Score: 408
Period size: 94 Copynumber: 3.1 Consensus size: 94
89750 AAATTGGCTC
* * *
89760 TGAAATTGGGAAGTTGTTTATTGACAACTAGCGGTCCCTTCGTCATGAAGTTGAACTTGCATTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGT
* *
89825 CTTGAGTCCAATATCCTTCGCTATGAAGT
66 CTGGAGTCCAATATCCTTCGCTGTGAAGT
89854 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGT
*
89919 CTGGAGTCCAATATCCTTCGTTGTGAAGT
66 CTGGAGTCCAATATCCTTCGCTGTGAAGT
*
89948 TGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
1 TGAAATT-G----G-----GA-AA-TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
** *
90013 AACTTGTGTTGTCTGGAGTCCAATATCCTTCACTGTGAAGT
54 AACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
90054 TGAAATTGG
1 TGAAATTGG
90063 CTCTGAATTT
Statistics
Matches: 186, Mismatches: 11, Indels: 17
0.87 0.05 0.08
Matches are distributed among these distances:
94 95 0.51
95 1 0.01
99 1 0.01
101 1 0.01
104 2 0.01
105 3 0.02
106 83 0.45
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (94 bp):
TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGT
CTGGAGTCCAATATCCTTCGCTGTGAAGT
Found at i:91091 original size:22 final size:22
Alignment explanation
Indices: 91037--91091 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
91027 TTGTGTTTGG
*
91037 TCAAAGGTTTAGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
91059 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
91081 TCAAAGGTTTG
1 TCAAAGGTTTG
91092 ATGGGGTAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:91750 original size:19 final size:19
Alignment explanation
Indices: 91709--91758 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
91699 TCTTTTTGAT
** *
91709 TTTTGTTCTTTTTTTTTTG
1 TTTTGTTCTTTTTTGCTTC
91728 TTTTGTTCTTTTTTGCTTC
1 TTTTGTTCTTTTTTGCTTC
91747 TTTT-TT-TTTTTT
1 TTTTGTTCTTTTTT
91759 CTGTTTTTGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 6 0.21
18 2 0.07
19 20 0.71
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.84
Consensus pattern (19 bp):
TTTTGTTCTTTTTTGCTTC
Found at i:91750 original size:29 final size:29
Alignment explanation
Indices: 91708--91763 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
91698 TTCTTTTTGA
91708 TTTTTGTTCTTTTTTTTTTGTTT-TGTTCT
1 TTTTTGTTCTTTTTTTTTT-TTTCTGTTCT
91737 TTTTTGCTTC-TTTTTTTTTTTTCTGTT
1 TTTTTG-TTCTTTTTTTTTTTTTCTGTT
91764 TTTGCCCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 3 0.12
29 19 0.76
30 3 0.12
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (29 bp):
TTTTTGTTCTTTTTTTTTTTTTCTGTTCT
Found at i:91755 original size:16 final size:15
Alignment explanation
Indices: 91698--91757 Score: 61
Period size: 15 Copynumber: 3.9 Consensus size: 15
91688 TTGTCCATTT
*
91698 TTCTTTTTGATTTTTG
1 TTCTTTTT-TTTTTTG
91714 TTC-TTTTTTTTTTG
1 TTCTTTTTTTTTTTG
*
91728 TT-TTGTTCTTTTTTG
1 TTCTT-TTTTTTTTTG
91743 CTTCTTTTTTTTTTT
1 -TTCTTTTTTTTTTT
91758 TCTGTTTTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 9 0.24
15 13 0.35
16 13 0.35
17 2 0.05
ACGTcount: A:0.02, C:0.08, G:0.08, T:0.82
Consensus pattern (15 bp):
TTCTTTTTTTTTTTG
Found at i:91758 original size:27 final size:25
Alignment explanation
Indices: 91695--91767 Score: 67
Period size: 30 Copynumber: 2.8 Consensus size: 25
91685 TTTTTGTCCA
*
91695 TTTTTCTTTTTGATTTTTGTTCTTT
1 TTTTTTTTTTTGATTTTTGTTCTTT
*
91720 TTTTTTTGTTTTGTTCTTTTTTGCTTCTTT
1 TTTTTTT-TTTTG---ATTTTTG-TTCTTT
*
91750 TTTTTTTTTCTG-TTTTTG
1 TTTTTTTTTTTGATTTTTG
91768 CCCTTTTTGT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
25 12 0.30
26 5 0.12
29 10 0.25
30 13 0.32
ACGTcount: A:0.01, C:0.08, G:0.10, T:0.81
Consensus pattern (25 bp):
TTTTTTTTTTTGATTTTTGTTCTTT
Found at i:91773 original size:24 final size:26
Alignment explanation
Indices: 91721--91775 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
91711 TTGTTCTTTT
*
91721 TTTTTTGTTTTGTTCTTTTTTGCTTC
1 TTTTTTGTTTTGTTCTTTTTTGCTCC
91747 TTTTTT-TTTT-TTCTGTTTTTGC-CC
1 TTTTTTGTTTTGTTCT-TTTTTGCTCC
91771 TTTTT
1 TTTTT
91776 GTTCTAATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 10 0.37
25 11 0.41
26 6 0.22
ACGTcount: A:0.00, C:0.13, G:0.09, T:0.78
Consensus pattern (26 bp):
TTTTTTGTTTTGTTCTTTTTTGCTCC
Found at i:102721 original size:30 final size:30
Alignment explanation
Indices: 102687--102768 Score: 85
Period size: 31 Copynumber: 2.7 Consensus size: 30
102677 CTTTTTCATT
*
102687 TAAGTATCTAAAATATTTTTTTTATCAAAA
1 TAAGTATCTAAAATATTTTTTTGATCAAAA
* * *
102717 TAAGTAT-TCAAAGTTATCTTTTTGGTCAAAA
1 TAAGTATCT-AAA-ATATTTTTTTGATCAAAA
* *
102748 TAAGTACCTAAAGTATTTTTT
1 TAAGTATCTAAAATATTTTTT
102769 GGTCAAGATA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
29 1 0.02
30 17 0.40
31 23 0.55
32 1 0.02
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.45
Consensus pattern (30 bp):
TAAGTATCTAAAATATTTTTTTGATCAAAA
Found at i:102784 original size:29 final size:29
Alignment explanation
Indices: 102687--102793 Score: 101
Period size: 29 Copynumber: 3.6 Consensus size: 29
102677 CTTTTTCATT
* * **
102687 TAAGTATCTAAAATATTTTTTTTATCAAAA
1 TAAGTACCTAAAGTA-TTTTTTGGTCAAAA
*
102717 TAAGTA-TTCAAAGTTATCTTTTTGGTCAAAA
1 TAAGTACCT-AAAG-TAT-TTTTTGGTCAAAA
*
102748 TAAGTACCTAAAGTATTTTTTGGTCAAGA
1 TAAGTACCTAAAGTATTTTTTGGTCAAAA
102777 T-AGATACCTAAAGTATT
1 TAAG-TACCTAAAGTATT
102794 CAATATTTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
28 2 0.03
29 27 0.41
30 13 0.20
31 23 0.35
32 1 0.02
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.41
Consensus pattern (29 bp):
TAAGTACCTAAAGTATTTTTTGGTCAAAA
Found at i:107543 original size:29 final size:30
Alignment explanation
Indices: 107499--107562 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
107489 AAAGAGAAAT
107499 TAAATTTTAACATATTCAT-AAACATTTATA
1 TAAATTTTAACATATTCATAAAACATTTA-A
* * *
107529 TAAATTTT-ATATATTTATAAAATATTTAA
1 TAAATTTTAACATATTCATAAAACATTTAA
107558 TAAAT
1 TAAAT
107563 GATTATTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 14 0.47
30 16 0.53
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (30 bp):
TAAATTTTAACATATTCATAAAACATTTAA
Found at i:108089 original size:29 final size:29
Alignment explanation
Indices: 107978--108078 Score: 123
Period size: 29 Copynumber: 3.5 Consensus size: 29
107968 CCCAACCCAT
****
107978 AGGTCGCCATGCACTCCCA-GCGACCTCCT
1 AGGTCGCCATGCACT-CCAGGCGACCAAGG
* *
108007 AGGTCGCCATGCACTCCGGGCGACCAATG
1 AGGTCGCCATGCACTCCAGGCGACCAAGG
*
108036 AGGTCGTCATGCACTCCAGGCGACCAAGG
1 AGGTCGCCATGCACTCCAGGCGACCAAGG
108065 AGGTCGCCATGCAC
1 AGGTCGCCATGCAC
108079 GCCCGACGAC
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
28 2 0.03
29 60 0.97
ACGTcount: A:0.21, C:0.37, G:0.28, T:0.15
Consensus pattern (29 bp):
AGGTCGCCATGCACTCCAGGCGACCAAGG
Found at i:114657 original size:30 final size:30
Alignment explanation
Indices: 114616--114679 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
114606 AATACCATTC
114616 AAAACAAAAATCAAATTAAACCTCACAGAT
1 AAAACAAAAATCAAATTAAACCTCACAGAT
*
114646 AAAAGAAAAATCAAATTAAACCTCACAGAT
1 AAAACAAAAATCAAATTAAACCTCACAGAT
114676 AAAA
1 AAAA
114680 AGGGGAAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.62, C:0.17, G:0.05, T:0.16
Consensus pattern (30 bp):
AAAACAAAAATCAAATTAAACCTCACAGAT
Done.