Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008273.1 Hibiscus syriacus cultivar Beakdansim tig00110930_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: 1042195
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:842905 original size:11 final size:11
Alignment explanation
Indices: 842874--842907 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
842864 ATCGAATAGA
*
842874 CTCGACTTGAG
1 CTCGACTCGAG
842885 CTCGAGCTCGAG
1 CTCGA-CTCGAG
842897 CTCGACTCGAG
1 CTCGACTCGAG
842908 TTCTTAACGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.18, C:0.32, G:0.29, T:0.21
Consensus pattern (11 bp):
CTCGACTCGAG
Found at i:844065 original size:3 final size:3
Alignment explanation
Indices: 844057--844081 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
844047 GGTGGAGGTT
844057 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
844082 CCACTTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:844398 original size:28 final size:26
Alignment explanation
Indices: 844341--844405 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 26
844331 TGAAGATAAA
844341 ATATTATAAAA--TTATAATATATAT
1 ATATTATAAAATTTTATAATATATAT
*
844365 ATATTATTAAATTTTATAATATATAT
1 ATATTATAAAATTTTATAATATATAT
844391 ATAAATTATAAAATT
1 AT--ATTATAAAATT
844406 ACAATACACT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 10 0.29
26 15 0.43
28 10 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
ATATTATAAAATTTTATAATATATAT
Found at i:845184 original size:30 final size:30
Alignment explanation
Indices: 845102--845177 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 30
845092 GTTCATATAT
*
845102 CATATTCGA-CATTTTGACAAAGTCATGTAC
1 CATATT-GAGCATTTTAACAAAGTCATGTAC
* *
845132 CATATTGGGGATTTTAACAAAGTACATGTAC
1 CATATTGAGCATTTTAACAAAGT-CATGTAC
845163 CATATT-AGCATTTTA
1 CATATTGAGCATTTTA
845178 TTAAAGTTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
29 1 0.03
30 25 0.64
31 13 0.33
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (30 bp):
CATATTGAGCATTTTAACAAAGTCATGTAC
Found at i:850422 original size:21 final size:21
Alignment explanation
Indices: 850398--850442 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
850388 AATAGGAAAT
850398 AAGAGAACGG-AATGGTAAGAA
1 AAGA-AACGGAAATGGTAAGAA
*
850419 AAGACACGGCAAATGGTAAGAA
1 AAGAAACGG-AAATGGTAAGAA
850441 AA
1 AA
850443 ATATGACATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 4 0.19
21 4 0.19
22 13 0.62
ACGTcount: A:0.53, C:0.09, G:0.29, T:0.09
Consensus pattern (21 bp):
AAGAAACGGAAATGGTAAGAA
Found at i:857410 original size:55 final size:56
Alignment explanation
Indices: 857326--857434 Score: 184
Period size: 55 Copynumber: 1.9 Consensus size: 56
857316 TCTCAACGCT
*
857326 CGTGATGGTTGGAAACTGTCACTAACCATCTCATTT-AACTATCGCCAAGGACACA
1 CGTGATGGTCGGAAACTGTCACTAACCATCTCATTTAAACTATCGCCAAGGACACA
*
857381 CGTGATGGTCGGAAACTGTCACTAACCATCTCATTTACAACTATTGCCAAGGAC
1 CGTGATGGTCGGAAACTGTCACTAACCATCTCATTTA-AACTATCGCCAAGGAC
857435 GAAAGCAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
55 35 0.70
57 15 0.30
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (56 bp):
CGTGATGGTCGGAAACTGTCACTAACCATCTCATTTAAACTATCGCCAAGGACACA
Found at i:864807 original size:158 final size:159
Alignment explanation
Indices: 864519--864836 Score: 613
Period size: 158 Copynumber: 2.0 Consensus size: 159
864509 CAGAATGCCC
864519 TGAAGAAAGATTTGAAGGCCCTTGCGGCAGTTGCACTTATGCACATAATGAATCCAAACCAGTGA
1 TGAAGAAAGATTTGAAGGCCCTTGCGGCAGTTGCACTTATGCACATAATGAATCCAAACCAGTGA
864584 AAACCTGGTTCACCCTGCCACAAAATTCATTAACCAAATAAGTTCTTAAAAAGAAATAAAGGTAC
66 AAACCTGGTTCACCCTGCCACAAAATTCATTAACCAAATAAGTTCTTAAAAAGAAATAAAGGTAC
864649 TGTAGAACTGCTGAAAG-TGCTTAGATTT
131 TGTAGAACTGCTGAAAGTTGCTTAGATTT
864677 TGAAGAACAGA-TTGAAGGCCCTTGCGGCAGTTGCACTTATGCACATAATGAATCCAAACCAGTG
1 TGAAGAA-AGATTTGAAGGCCCTTGCGGCAGTTGCACTTATGCACATAATGAATCCAAACCAGTG
864741 AAAACCTGGTTCACCCTGCCACAAAATTCATTAACCAAATAAGTTCTTAAAAAGAAATAAAGGTA
65 AAAACCTGGTTCACCCTGCCACAAAATTCATTAACCAAATAAGTTCTTAAAAAGAAATAAAGGTA
864806 CTGTAGAACTGCTGAAAGTTGCTTAGATTT
130 CTGTAGAACTGCTGAAAGTTGCTTAGATTT
864836 T
1 T
864837 TGTCTCTTTC
Statistics
Matches: 158, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
158 143 0.91
159 15 0.09
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.25
Consensus pattern (159 bp):
TGAAGAAAGATTTGAAGGCCCTTGCGGCAGTTGCACTTATGCACATAATGAATCCAAACCAGTGA
AAACCTGGTTCACCCTGCCACAAAATTCATTAACCAAATAAGTTCTTAAAAAGAAATAAAGGTAC
TGTAGAACTGCTGAAAGTTGCTTAGATTT
Found at i:867228 original size:16 final size:17
Alignment explanation
Indices: 867199--867236 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
867189 AGTTTACAAT
867199 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
867215 TAATTATAAA-AATATC
1 TAATTATAAATAATATC
867231 TAATTA
1 TAATTA
867237 ATTTGATTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:867359 original size:9 final size:9
Alignment explanation
Indices: 867345--867370 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
867335 ATTCGGTCGG
867345 TCGATTAAT
1 TCGATTAAT
867354 TCGATTAAT
1 TCGATTAAT
867363 TCGATTAA
1 TCGATTAA
867371 AACCGAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (9 bp):
TCGATTAAT
Found at i:869978 original size:28 final size:28
Alignment explanation
Indices: 869893--869985 Score: 80
Period size: 28 Copynumber: 3.3 Consensus size: 28
869883 AAAGGATAAT
*
869893 TAGTTTAGGGCTTATTTTGACC-AAAAA
1 TAGTTTAGGACTTATTTTGACCAAAAAA
*** ** * *
869920 TAGTTTAGGTACTTAAAGTGGTCACATAA
1 TAGTTTAGG-ACTTATTTTGACCAAAAAA
*
869949 TAGTTAAGGACTTATTTTGACCAAAAAA
1 TAGTTTAGGACTTATTTTGACCAAAAAA
*
869977 TAATTTAGG
1 TAGTTTAGG
869986 GGCTTAAAGC
Statistics
Matches: 46, Mismatches: 18, Indels: 3
0.69 0.27 0.04
Matches are distributed among these distances:
27 9 0.20
28 26 0.57
29 11 0.24
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (28 bp):
TAGTTTAGGACTTATTTTGACCAAAAAA
Found at i:872199 original size:20 final size:20
Alignment explanation
Indices: 872176--872215 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
872166 ATAATAATGA
872176 AAGTTTCTATAGCATTTAAC
1 AAGTTTCTATAGCATTTAAC
*
872196 AAGTTTCTATAGGATTTAAC
1 AAGTTTCTATAGCATTTAAC
872216 CTGCAAGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (20 bp):
AAGTTTCTATAGCATTTAAC
Found at i:876058 original size:40 final size:38
Alignment explanation
Indices: 876014--876099 Score: 91
Period size: 40 Copynumber: 2.2 Consensus size: 38
876004 GATAATCTAT
* * **
876014 AATGTTATATTATTTATAATATTTTTTGTTGACAACCGAA
1 AATGTTATATTATTCATAACATTTTAGGTT--CAACCGAA
** *
876054 AATGTTACCTTATTCGTAACATTTTAGGTTCAACCGAA
1 AATGTTATATTATTCATAACATTTTAGGTTCAACCGAA
876092 AATGTTAT
1 AATGTTAT
876100 GAATAATGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
38 15 0.39
40 23 0.61
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.43
Consensus pattern (38 bp):
AATGTTATATTATTCATAACATTTTAGGTTCAACCGAA
Found at i:877270 original size:2 final size:2
Alignment explanation
Indices: 877263--877297 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
877253 CTTTTTATTA
877263 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
877298 ATTCTCCTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:897727 original size:24 final size:23
Alignment explanation
Indices: 897693--897742 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 23
897683 AATGTCATTG
*
897693 AAAAAATTTAA-CAATTAACGTT
1 AAAAAATTTAATCAATTAACGAT
*
897715 AAAAAACTCTTAATCATTTAACGAT
1 AAAAAA-T-TTAATCAATTAACGAT
897740 AAA
1 AAA
897743 CATTTCTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 6 0.26
23 1 0.04
24 4 0.17
25 12 0.52
ACGTcount: A:0.54, C:0.12, G:0.04, T:0.30
Consensus pattern (23 bp):
AAAAAATTTAATCAATTAACGAT
Found at i:900483 original size:420 final size:420
Alignment explanation
Indices: 899704--900947 Score: 2068
Period size: 420 Copynumber: 3.0 Consensus size: 420
899694 AAGTGTTGCG
* *
899704 ACAACGAGTAGGGGTGTAAAAAGTTTTTTCTCAACCCCTGCCAGTCGTCAAAGATCGAACAACCA
1 ACAACGAGTAGGGGTGTAACAAGTTTTTTCTCAACCCCTGCCAGTCCTCAAAGATCGAACAACCA
*
899769 AGATCATTTTTACTCTTATGATGATGCAGATTCAGCCAAATCTTCCTTAAGTCGTCACAGGGGCT
66 AGATCATTTTTACTCTTATGATGATGCAGATTCAGCCAAATCTTCCTTAAGTCGTCGCAGGGGCT
*
899834 TCTCTCCTAAGAATTATGGGAGTGTTGACCACAACTTGAGGCTGAATGTGCATCCCAGGAGTGCT
131 TCTCTCCTGAGAATTATGGGAGTGTTGACCACAACTTGAGGCTGAATGTGCATCCCAGGAGTGCT
*
899899 CCAACAACGGCTTTATCTAGTCCTTCCGTTAGCCCCCAAAGATCAAAAACAGTAGGTCCTTTTCA
196 CCAACAACGGCTTTATCTAGTCCTTCCGTTAGCCCCCAAAGATCAAGAACAGTAGGTCCTTTTCA
*
899964 TTCAGACCACCTGGTGCTGCTTCAAAACAATCTGCAGGAAAATGCATATCCATTGCCCCTTCCCC
261 TTCAGACCATCTGGTGCTGCTTCAAAACAATCTGCAGGAAAATGCATATCCATTGCCCCTTCCCC
* * * *
900029 CTGGAGGTTTACAGCCGTCACAATCACCTTTGCCACGATCGTCACCTGTTTCAAATCACATAATA
326 CTGGAGCTTTACAGCCATCACAATCACCTTTGCCACGAACGTCACCTGTTTCAAATCACTTAATA
*
900094 GAAAAACCAATCACAAAGCTAATAGTCGAC
391 GAAAAACCAATCACAAAGCCAATAGTCGAC
* *
900124 ACAACGAGTAGGGGTGTAACAAGTGTTTTCTCAACCCCTGCTAGTCCTCAAAGATCGAACAACCA
1 ACAACGAGTAGGGGTGTAACAAGTTTTTTCTCAACCCCTGCCAGTCCTCAAAGATCGAACAACCA
* *
900189 AGATCATTTTTACTCTTATGATGACGCAGATTCAGCCAAATCCTCCTTAAGTCGTCGCAGGGGCT
66 AGATCATTTTTACTCTTATGATGATGCAGATTCAGCCAAATCTTCCTTAAGTCGTCGCAGGGGCT
*
900254 TCTCTCCTGAGAATTATTGGAGTGTTGACCACAACTTGAGGCTGAATGTGCATCCCAGGAGTGCT
131 TCTCTCCTGAGAATTATGGGAGTGTTGACCACAACTTGAGGCTGAATGTGCATCCCAGGAGTGCT
*
900319 CCAACAACGGCTTTATCTAGTCCTTCCATTAGCCCCCAAAGATCAAGAACAGTAGGTCCTTTTCA
196 CCAACAACGGCTTTATCTAGTCCTTCCGTTAGCCCCCAAAGATCAAGAACAGTAGGTCCTTTTCA
900384 TTCAGACCATCTGGTGCTGCTTCAAAACAATCTGCAGGAAAATGCATATCCATTGCCCCTTCCCC
261 TTCAGACCATCTGGTGCTGCTTCAAAACAATCTGCAGGAAAATGCATATCCATTGCCCCTTCCCC
*
900449 CTGGAGCTTTACAGCCATCACAATCACCTTTGCCACGACCGTCACCTGTTTCAAATCACTTAATA
326 CTGGAGCTTTACAGCCATCACAATCACCTTTGCCACGAACGTCACCTGTTTCAAATCACTTAATA
*
900514 GAAAAACCAATCACAAAGCCAATAGTCGCC
391 GAAAAACCAATCACAAAGCCAATAGTCGAC
900544 ACAACGAGTAGGGGTGTAACAAGTTTTTTCTCAACCCCTGCCAGTCCTCAAAGATCGAACAACCA
1 ACAACGAGTAGGGGTGTAACAAGTTTTTTCTCAACCCCTGCCAGTCCTCAAAGATCGAACAACCA
* ** *
900609 AGATCATTTTTACTCTTATGATGTTGCAGATTCAGCCAAATCTTTATTAAGTCATCGCAGGGGCT
66 AGATCATTTTTACTCTTATGATGATGCAGATTCAGCCAAATCTTCCTTAAGTCGTCGCAGGGGCT
* * *
900674 TCTCTCTTGAGAATTATGGGAGTGTTTACCACAACTTGAGGCTGAATGTTCATCCCAGGAGTGCT
131 TCTCTCCTGAGAATTATGGGAGTGTTGACCACAACTTGAGGCTGAATGTGCATCCCAGGAGTGCT
* **
900739 CCAACAACGGCTTTTTCTAGTCC-T--GTTAGCCCGAAAAGATCAAGAACAGTAGGTCCTTTTCA
196 CCAACAACGGCTTTATCTAGTCCTTCCGTTAGCCCCCAAAGATCAAGAACAGTAGGTCCTTTTCA
* * * **
900801 TTCAGACCATTCTGAGTG--GCTTCAAAACAATCGGCAAGTAAATGTGTATCCATTGCCCCTTCC
261 TTCAGACCA-TCTG-GTGCTGCTTCAAAACAATCTGCAGGAAAATGCATATCCATTGCCCCTTCC
* * * *
900864 CCCTGGAGCTTTACCGCCATCACAATCACGTTTTCCAC-AACTGTCACCAGTTTCAAATCACTTA
324 CCCTGGAGCTTTACAGCCATCACAATCACCTTTGCCACGAAC-GTCACCTGTTTCAAATCACTTA
*
900928 ATAGAAAAGCCAATCACAAA
388 ATAGAAAAACCAATCACAAA
900948 CTCAATGATA
Statistics
Matches: 776, Mismatches: 45, Indels: 9
0.93 0.05 0.01
Matches are distributed among these distances:
416 2 0.00
417 159 0.20
418 4 0.01
419 4 0.01
420 607 0.78
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.27
Consensus pattern (420 bp):
ACAACGAGTAGGGGTGTAACAAGTTTTTTCTCAACCCCTGCCAGTCCTCAAAGATCGAACAACCA
AGATCATTTTTACTCTTATGATGATGCAGATTCAGCCAAATCTTCCTTAAGTCGTCGCAGGGGCT
TCTCTCCTGAGAATTATGGGAGTGTTGACCACAACTTGAGGCTGAATGTGCATCCCAGGAGTGCT
CCAACAACGGCTTTATCTAGTCCTTCCGTTAGCCCCCAAAGATCAAGAACAGTAGGTCCTTTTCA
TTCAGACCATCTGGTGCTGCTTCAAAACAATCTGCAGGAAAATGCATATCCATTGCCCCTTCCCC
CTGGAGCTTTACAGCCATCACAATCACCTTTGCCACGAACGTCACCTGTTTCAAATCACTTAATA
GAAAAACCAATCACAAAGCCAATAGTCGAC
Found at i:903634 original size:20 final size:20
Alignment explanation
Indices: 903597--903634 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
903587 GAATCATAAG
*
903597 TTTTGATCCTGCATGAGTTT
1 TTTTGATCCTGCACGAGTTT
903617 TTTTGAT-CTGTCACGAGT
1 TTTTGATCCTG-CACGAGT
903635 CTGACCTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.16, C:0.16, G:0.21, T:0.47
Consensus pattern (20 bp):
TTTTGATCCTGCACGAGTTT
Found at i:904567 original size:17 final size:17
Alignment explanation
Indices: 904540--904590 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 17
904530 TAAATGAATG
*
904540 TAATAAGATAATATATAA
1 TAATAAAATAATA-ATAA
904558 T-ATAAAATAATAATAA
1 TAATAAAATAATAATAA
*
904574 TAATAAAATAAAAATAA
1 TAATAAAATAATAATAA
904591 AAAATCAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
16 5 0.17
17 24 0.80
18 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (17 bp):
TAATAAAATAATAATAA
Found at i:904587 original size:23 final size:23
Alignment explanation
Indices: 904547--904590 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
904537 ATGTAATAAG
*
904547 ATAATATATAATATAAAATAATA
1 ATAATATAAAATATAAAATAATA
904570 ATAATAATAAAATA-AAAATAA
1 ATAAT-ATAAAATATAAAATAA
904591 AAAATCAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (23 bp):
ATAATATAAAATATAAAATAATA
Found at i:931040 original size:12 final size:12
Alignment explanation
Indices: 931023--931047 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
931013 GTCAAATAAT
931023 TTAGGCACCAAA
1 TTAGGCACCAAA
931035 TTAGGCACCAAA
1 TTAGGCACCAAA
931047 T
1 T
931048 GGTGCTTTGT
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:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (12 bp):
TTAGGCACCAAA
Found at i:934110 original size:25 final size:26
Alignment explanation
Indices: 934076--934141 Score: 116
Period size: 26 Copynumber: 2.6 Consensus size: 26
934066 AAATGCCTCT
934076 TTAATTTCAATATAC-TTTTTAATAG
1 TTAATTTCAATATACTTTTTTAATAG
*
934101 TTAATTTCAATAAACTTTTTTAATAG
1 TTAATTTCAATATACTTTTTTAATAG
934127 TTAATTTCAATATAC
1 TTAATTTCAATATAC
934142 GTTGTTCCTA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
25 14 0.37
26 24 0.63
ACGTcount: A:0.38, C:0.09, G:0.03, T:0.50
Consensus pattern (26 bp):
TTAATTTCAATATACTTTTTTAATAG
Found at i:934454 original size:30 final size:30
Alignment explanation
Indices: 934420--934479 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
934410 TAATCATGCT
934420 TCGATGAAAAGCCGATGCAAAATCCAAAGA
1 TCGATGAAAAGCCGATGCAAAATCCAAAGA
934450 TCGATGAAAAGCCGATGCAAAATCCAAAGA
1 TCGATGAAAAGCCGATGCAAAATCCAAAGA
934480 GAAACATAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.13
Consensus pattern (30 bp):
TCGATGAAAAGCCGATGCAAAATCCAAAGA
Found at i:941438 original size:2 final size:2
Alignment explanation
Indices: 941433--941459 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
941423 CAACAATTTA
941433 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
941460 CTACTTCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:958256 original size:25 final size:25
Alignment explanation
Indices: 958228--958284 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
958218 TTTATAATTA
958228 AAATTTTATATAAAATTCAAAGATT
1 AAATTTTATATAAAATTCAAAGATT
* * *
958253 AAATTTTTTATGAAGTTCAAAGATT
1 AAATTTTATATAAAATTCAAAGATT
*
958278 AATTTTT
1 AAATTTT
958285 TTTACTCTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.46
Consensus pattern (25 bp):
AAATTTTATATAAAATTCAAAGATT
Found at i:958318 original size:14 final size:14
Alignment explanation
Indices: 958299--958326 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
958289 CTCTTTCATT
958299 AATTTTTTTTTATA
1 AATTTTTTTTTATA
958313 AATTTTTTTTTATA
1 AATTTTTTTTTATA
958327 TTTTTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
AATTTTTTTTTATA
Found at i:968941 original size:13 final size:13
Alignment explanation
Indices: 968907--968968 Score: 67
Period size: 13 Copynumber: 4.9 Consensus size: 13
968897 AAACGAACAC
*
968907 AAACGAACAAACAT
1 AAACGAACATA-AT
968921 AAACGAACATAAT
1 AAACGAACATAAT
*
968934 AAATGAAC---AT
1 AAACGAACATAAT
968944 AAACGAACATAAT
1 AAACGAACATAAT
*
968957 AAATGAACATAA
1 AAACGAACATAA
968969 ACGAGCAACA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
10 9 0.22
13 22 0.54
14 10 0.24
ACGTcount: A:0.63, C:0.15, G:0.08, T:0.15
Consensus pattern (13 bp):
AAACGAACATAAT
Found at i:968946 original size:23 final size:23
Alignment explanation
Indices: 968916--968972 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
968906 CAAACGAACA
968916 AACATAAACGAACATAATAAATG
1 AACATAAACGAACATAATAAATG
968939 AACATAAACGAACATAATAAATG
1 AACATAAACGAACATAATAAATG
968962 AACATAAACGA
1 AACATAAACGA
968973 GCAACACAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.61, C:0.14, G:0.09, T:0.16
Consensus pattern (23 bp):
AACATAAACGAACATAATAAATG
Found at i:969266 original size:24 final size:26
Alignment explanation
Indices: 969235--969290 Score: 98
Period size: 24 Copynumber: 2.2 Consensus size: 26
969225 TACCATCTGT
969235 TCGAACATAAATGAACGAACATA-AA
1 TCGAACATAAATGAACGAACATATAA
969260 T-GAACATAAATGAACGAACATATAA
1 TCGAACATAAATGAACGAACATATAA
969285 TCGAAC
1 TCGAAC
969291 GTTCACGAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
24 21 0.72
25 4 0.14
26 4 0.14
ACGTcount: A:0.54, C:0.16, G:0.12, T:0.18
Consensus pattern (26 bp):
TCGAACATAAATGAACGAACATATAA
Found at i:969290 original size:16 final size:14
Alignment explanation
Indices: 969236--969291 Score: 66
Period size: 14 Copynumber: 4.1 Consensus size: 14
969226 ACCATCTGTT
969236 CGAACATAAATGAA
1 CGAACATAAATGAA
969250 CGAACATAAAT---
1 CGAACATAAATGAA
969261 -GAACATAAATGAA
1 CGAACATAAATGAA
969274 CGAACATATAATCGAA
1 CGAACATA-AAT-GAA
969290 CG
1 CG
969292 TTCACGAACG
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
10 10 0.28
14 18 0.50
15 3 0.08
16 5 0.14
ACGTcount: A:0.54, C:0.16, G:0.14, T:0.16
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:980029 original size:36 final size:36
Alignment explanation
Indices: 979989--980095 Score: 151
Period size: 36 Copynumber: 3.0 Consensus size: 36
979979 AATACAATTT
* *
979989 ACAATAAATTATGTCACTTGATAAATAGACTTATTA
1 ACAATAAGTCATGTCACTTGATAAATAGACTTATTA
* *
980025 ACAATAAGTCATGACACTTGATAAATAGACTAATTA
1 ACAATAAGTCATGTCACTTGATAAATAGACTTATTA
* * *
980061 ATAATAAGTCATGTCACTTGGTAACTAGACTTATT
1 ACAATAAGTCATGTCACTTGATAAATAGACTTATT
980096 CTTAGTTTAA
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 62 1.00
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (36 bp):
ACAATAAGTCATGTCACTTGATAAATAGACTTATTA
Found at i:986372 original size:741 final size:744
Alignment explanation
Indices: 984878--987831 Score: 5710
Period size: 741 Copynumber: 4.0 Consensus size: 744
984868 AATTCTCAGC
*
984878 AACTCCATATATAGCATTAAAACAGAAAAAAGGCCAATAGCACTCCTATTGATTAACACCCTAGT
1 AACTACATATATAGCATTAAAACAGAAAAAAGGCCAATAGCACTCCTATTGATTAACACCCTAGT
984943 TATTGTTTGA---GTATAT-AAACTACACTTGGTTTTGAATTATGAGGTTCAAAGTCCTAGGCAC
66 TATTGTTTGAGTTGTATATAAAACTACACTT-GTTTTGAATTATGAGGTTCAAAGTCCTAGGCAC
985004 GCACTCCTGTTTCCATTCTCCCAGTAATTTGACGATCATATGGCTAATTACACCAATAGGTAGGA
130 GCACTCCTGTTTCCATTCTCCCAGTAATTTGACGATCATATGGCTAATTACACCAATAGGTAGGA
985069 AGTAAATTGCTTC-TTT-TAGTCAAGCA-CCACCCAATATCCTTTTGAGGTTATGGTTGACAAAC
195 AGTAAATTGCTTCTTTTATAGTCAAGCACCCACCCAATATCCTTTTGAGGTTATGGTTGACAAAC
985131 TGCACAACCTTATTTA-TTTCTTCACTACGCTTGGATCAAGAACAAGGTTTTTAACTTGCAA-TT
260 TGCACAACCTTATTTATTTTCTTCACTACGCTTGGATCAAGAACAAGGTTTTTAACTTGCAATTT
985194 TTTT-TATGAGAATTTTGACCAAAAGATAAGAGAAAGGAAAGGTAAGCTAGAAAAGGAAATCCTC
325 TTTTCTATGAGAATTTTGACCAAAAGATAAGAGAAAGGAAAGGTAAGCTAGAAAAGGAAATCCTC
985258 ATTATACCTTTCTATGAAACAAAGCATCAATAATGTACAAAATTTCCAAAGTGCTTGAAGTACAT
390 ATTATACCTTTCTATGAAACAAAGCATCAATAATGTACAAAATTTCCAAAGTGCTTGAAGTACAT
985323 CAATTTTGGAACAGGCAGAGTGAGGTAGGTGCAGTTTATATCTTACCATTAACCAGGATAAATAA
455 CAATTTTGGAACAGGCAGAGTGAGGTAGGTGCAGTTTATATCTTACCATTAACCAGGATAAATAA
985388 TACACATTGAACATACAGAGCCAAATTTGAAGGAAATTATTCATCTGTCTGAAACATAAACATGA
520 TACACATTGAACATACAGAGCCAAATTTGAAGGAAATTATTCATCTGTCTGAAACATAAACATGA
985453 AGTTTTCAGCATATGGAATCTGATTGCTAAGTTAACACTCTGGGTAGACCAGGTGAACCAGAGAC
585 AGTTTTCAGCATATGGAATCTGATTGCTAAGTTAACACTCTGGGTAGACCAGGTGAACCAGAGAC
*
985518 ATGTTTCAGCCAGAAAGTTGACTATTGAAGTGAGGTTAATATGCATTGAAGTTTTAATCAGAATG
650 ATGTTTCAGTCAGAAAGTTGACTATTGAAGTGAGGTTAATATGCATTGAAGTTTTAATCAGAATG
985583 TTGCATAAAAGAAGAAAAAAATGTATATAA
715 TTGCATAAAAGAAGAAAAAAATGTATATAA
985613 AACTACATATATAGCATTAAAACAGAAAAAAGGCCAATAGCACTCCTATTGATTAACACCCTAGT
1 AACTACATATATAGCATTAAAACAGAAAAAAGGCCAATAGCACTCCTATTGATTAACACCCTAGT
985678 TATTGTTTGAGTTGTATATAAAACTACACTTGTTTTGAATTATGAGGTTCAAAGTCCTAGGCACG
66 TATTGTTTGAGTTGTATATAAAACTACACTTGTTTTGAATTATGAGGTTCAAAGTCCTAGGCACG
985743 CACTCCTGTTTCCATTCTCCCAGTAATTTGACGATCATATGGCTAATTACACCAATAGGTAGGAA
131 CACTCCTGTTTCCATTCTCCCAGTAATTTGACGATCATATGGCTAATTACACCAATAGGTAGGAA
985808 GTAAATTGCTTCTTTTATAGTCAAGCACCCACCCAATATCCTTTTGAGGTTATGGTTGACAAACT
196 GTAAATTGCTTCTTTTATAGTCAAGCACCCACCCAATATCCTTTTGAGGTTATGGTTGACAAACT
985873 GCACAACCTTATTTATTTTCTTCACTACGCTTGGATCAAGAACAAGGTTTTTAACTTGCAATTTT
261 GCACAACCTTATTTATTTTCTTCACTACGCTTGGATCAAGAACAAGGTTTTTAACTTGCAATTTT
985938 TTTCTATGAGAATTTTGACCAAAAGATAAGAGAAAGGAAAGGTAAGCTAG-AAAGGAAAT-C-CA
326 TTTCTATGAGAATTTTGACCAAAAGATAAGAGAAAGGAAAGGTAAGCTAGAAAAGGAAATCCTCA
986000 TTATACCTTTCTATGAAACAAAGCATCAATAATGTACAAAATTTCCAAAGTGCTTGAAGTACATC
391 TTATACCTTTCTATGAAACAAAGCATCAATAATGTACAAAATTTCCAAAGTGCTTGAAGTACATC
986065 AATTTTGGAACAGGCAGAGTGAGGTAGGTGCAGTTTATATCTTACCATTAACCAGGATAAATAAT
456 AATTTTGGAACAGGCAGAGTGAGGTAGGTGCAGTTTATATCTTACCATTAACCAGGATAAATAAT
986130 ACACATTGAACATACAGAGCCAAATTTGAAGGAAATTATTCATCTGTCTGAAACATAAACATGAA
521 ACACATTGAACATACAGAGCCAAATTTGAAGGAAATTATTCATCTGTCTGAAACATAAACATGAA
986195 GTTTTCAGCATATGGAATCTGATTGCTAAGTTAACACTCTGGGTAGACCAGGTGAACCAGAGACA
586 GTTTTCAGCATATGGAATCTGATTGCTAAGTTAACACTCTGGGTAGACCAGGTGAACCAGAGACA
986260 TGTTTCAGTCAGAAAGTTGACTATTGAAGTGAGGTTAATATGCATTGAAGTTTTAATCAGAATGT
651 TGTTTCAGTCAGAAAGTTGACTATTGAAGTGAGGTTAATATGCATTGAAGTTTTAATCAGAATGT
986325 TGCATAAAAGAAGAAAAAAATGTATATAA
716 TGCATAAAAGAAGAAAAAAATGTATATAA
986354 AACTACATATATAGCATTAAAACAGAAAAAAGGCCAATAGCACTCCTATTGATTAACACCCTAGT
1 AACTACATATATAGCATTAAAACAGAAAAAAGGCCAATAGCACTCCTATTGATTAACACCCTAGT
986419 TATTGTTTGAGTTGTATATAAAACTACACTTGTTTTGAATTATGAGGTTCAAAGTCCTAGGCACG
66 TATTGTTTGAGTTGTATATAAAACTACACTTGTTTTGAATTATGAGGTTCAAAGTCCTAGGCACG
986484 CACTCCTGTTTCCATTCTCCCAGTAATTTGACGATCATATGGCTAATTACACCAATAGGTAGGAA
131 CACTCCTGTTTCCATTCTCCCAGTAATTTGACGATCATATGGCTAATTACACCAATAGGTAGGAA
986549 GTAAATTGCTTCTTTTATAGTCAAGCACCCACCCAATATCCTTTTGAGGTTATGGTTGACAAACT
196 GTAAATTGCTTCTTTTATAGTCAAGCACCCACCCAATATCCTTTTGAGGTTATGGTTGACAAACT
986614 GCACAACCTTATTTATTTTCTTCACTACGCTTGGATCAAGAACAAGGTTTTTAACTTGCAATTTT
261 GCACAACCTTATTTATTTTCTTCACTACGCTTGGATCAAGAACAAGGTTTTTAACTTGCAATTTT
986679 TTTCTATGAGAATTTTGACCAAAAGATAAGAGAAAGGAAAGGTAAGCTAGAAAAGGAAATCCTCA
326 TTTCTATGAGAATTTTGACCAAAAGATAAGAGAAAGGAAAGGTAAGCTAGAAAAGGAAATCCTCA
986744 TTATACCTTTCTATGAAACAAAGCATC-ATAATGTACAAAATTTCCAAAGTGCTTGAAGTACATC
391 TTATACCTTTCTATGAAACAAAGCATCAATAATGTACAAAATTTCCAAAGTGCTTGAAGTACATC
986808 AATTTTGGAACAGGCAGAGTGAGGTAGGTGCAGTTT-TATCTTACCATTAACCAGG-TAAATAAT
456 AATTTTGGAACAGGCAGAGTGAGGTAGGTGCAGTTTATATCTTACCATTAACCAGGATAAATAAT
*
986871 ACACATTGAACATATAGAGCCAAATTTGAAGGAAATTATTCATCTGTCTGAAACATAAACATGAA
521 ACACATTGAACATACAGAGCCAAATTTGAAGGAAATTATTCATCTGTCTGAAACATAAACATGAA
986936 GTTTTCAGCATATGGAATCTGATTGCTAAGTTAACACTCTGGGTAGACCAGGTGAACCAGAGACA
586 GTTTTCAGCATATGGAATCTGATTGCTAAGTTAACACTCTGGGTAGACCAGGTGAACCAGAGACA
987001 TGTTTCAGTCAGAAAGTTGACTATTGAAGTGAGGTTAATATGCATTGAAGTTTTAATCAGAATGT
651 TGTTTCAGTCAGAAAGTTGACTATTGAAGTGAGGTTAATATGCATTGAAGTTTTAATCAGAATGT
987066 TGCAT-AAA-AAGAAAAAAATGTATATAA
716 TGCATAAAAGAAGAAAAAAATGTATATAA
*
987093 AACTACATATATAGCATTAAAACAGAAAAAAGGCCAACAGCACTCCTATTGATTAACACCCTAGT
1 AACTACATATATAGCATTAAAACAGAAAAAAGGCCAATAGCACTCCTATTGATTAACACCCTAGT
987158 TATTGTTTGAGTTGTATATAAAACTACACTTGTTTTGAATTATGAGGTTCAAAGTCCTAGGCACG
66 TATTGTTTGAGTTGTATATAAAACTACACTTGTTTTGAATTATGAGGTTCAAAGTCCTAGGCACG
987223 CACTCCTGTTTCCATTCTCCCAGTAATTTGACGATCATATGGCTAATTACACCAATAGGTAGGAA
131 CACTCCTGTTTCCATTCTCCCAGTAATTTGACGATCATATGGCTAATTACACCAATAGGTAGGAA
987288 GTAAATTGCTTCTTTTATAGTCAAGCACCCACCCAATATCCTTTTGAGGTTATGGTTGACAAACT
196 GTAAATTGCTTCTTTTATAGTCAAGCACCCACCCAATATCCTTTTGAGGTTATGGTTGACAAACT
*
987353 GCACAACCTTATTTATTTTCTTCACTAAGCTTGGATCAAGAACAAGGTTTTTAACTTGCAATTTT
261 GCACAACCTTATTTATTTTCTTCACTACGCTTGGATCAAGAACAAGGTTTTTAACTTGCAATTTT
987418 TTTCTATGAGAATTTTGACCAAAAGATAAGAGAAAGGAAAGGTAAGCTAGAAAAGGAAATCCTCA
326 TTTCTATGAGAATTTTGACCAAAAGATAAGAGAAAGGAAAGGTAAGCTAGAAAAGGAAATCCTCA
987483 TTATACCTTTCTATGAAACAAAGCATCAATAATGTACAAAATTTCCAAAGTGCTTGAAGTACATC
391 TTATACCTTTCTATGAAACAAAGCATCAATAATGTACAAAATTTCCAAAGTGCTTGAAGTACATC
*
987548 AATTTTGGAACAGGCAGAGTGAGGTAGGTGCAGTTTATATCTTACCATTAACCAGGTTAAATAAT
456 AATTTTGGAACAGGCAGAGTGAGGTAGGTGCAGTTTATATCTTACCATTAACCAGGATAAATAAT
987613 ACACATTGAACATACAGAGCCAAATTTGAAGGAAATTATTCATCTGTCTGAAACATAAACATGAA
521 ACACATTGAACATACAGAGCCAAATTTGAAGGAAATTATTCATCTGTCTGAAACATAAACATGAA
987678 GTTTTCAGCATATGGAATCTGATTGCTAAGTTAACACTCTGGGTAGACCAGGTGAACCAGAGACA
586 GTTTTCAGCATATGGAATCTGATTGCTAAGTTAACACTCTGGGTAGACCAGGTGAACCAGAGACA
987743 TGTTTCAGTCAGAAAGTTGACTATTGAAGTGAGGTTAATATGCATTGAAGTTTTAATCAGAATGT
651 TGTTTCAGTCAGAAAGTTGACTATTGAAGTGAGGTTAATATGCATTGAAGTTTTAATCAGAATGT
*
987808 TGCATAAAAGAATAAAAAAATGTA
716 TGCATAAAAGAAGAAAAAAATGTA
987832 GGCAATAAGG
Statistics
Matches: 2194, Mismatches: 7, Indels: 27
0.98 0.00 0.01
Matches are distributed among these distances:
735 74 0.03
738 117 0.05
739 448 0.20
740 86 0.04
741 1008 0.46
742 281 0.13
743 92 0.04
744 88 0.04
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.30
Consensus pattern (744 bp):
AACTACATATATAGCATTAAAACAGAAAAAAGGCCAATAGCACTCCTATTGATTAACACCCTAGT
TATTGTTTGAGTTGTATATAAAACTACACTTGTTTTGAATTATGAGGTTCAAAGTCCTAGGCACG
CACTCCTGTTTCCATTCTCCCAGTAATTTGACGATCATATGGCTAATTACACCAATAGGTAGGAA
GTAAATTGCTTCTTTTATAGTCAAGCACCCACCCAATATCCTTTTGAGGTTATGGTTGACAAACT
GCACAACCTTATTTATTTTCTTCACTACGCTTGGATCAAGAACAAGGTTTTTAACTTGCAATTTT
TTTCTATGAGAATTTTGACCAAAAGATAAGAGAAAGGAAAGGTAAGCTAGAAAAGGAAATCCTCA
TTATACCTTTCTATGAAACAAAGCATCAATAATGTACAAAATTTCCAAAGTGCTTGAAGTACATC
AATTTTGGAACAGGCAGAGTGAGGTAGGTGCAGTTTATATCTTACCATTAACCAGGATAAATAAT
ACACATTGAACATACAGAGCCAAATTTGAAGGAAATTATTCATCTGTCTGAAACATAAACATGAA
GTTTTCAGCATATGGAATCTGATTGCTAAGTTAACACTCTGGGTAGACCAGGTGAACCAGAGACA
TGTTTCAGTCAGAAAGTTGACTATTGAAGTGAGGTTAATATGCATTGAAGTTTTAATCAGAATGT
TGCATAAAAGAAGAAAAAAATGTATATAA
Found at i:999451 original size:13 final size:13
Alignment explanation
Indices: 999433--999457 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
999423 ACATTCTAAA
999433 TTTAATTGTATTC
1 TTTAATTGTATTC
999446 TTTAATTGTATT
1 TTTAATTGTATT
999458 TTTTTTAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.04, G:0.08, T:0.64
Consensus pattern (13 bp):
TTTAATTGTATTC
Found at i:1000270 original size:14 final size:14
Alignment explanation
Indices: 1000248--1000289 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
1000238 ATTATTAAAG
1000248 TTTTGAGATTTTTT
1 TTTTGAGATTTTTT
* *
1000262 TTTTAAGATTGATTT
1 TTTTGAGATT-TTTT
1000277 TTTTGAG-TTTTTT
1 TTTTGAGATTTTTT
1000290 AAATATAAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 3 0.13
14 11 0.48
15 9 0.39
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (14 bp):
TTTTGAGATTTTTT
Found at i:1000302 original size:15 final size:14
Alignment explanation
Indices: 1000282--1000320 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
1000272 GATTTTTTTG
1000282 AGTTTTTTAAATATA
1 AGTTTTTTAAATA-A
*
1000297 AGTTTTTTTAATAA
1 AGTTTTTTAAATAA
1000311 A-TTTTTTAAA
1 AGTTTTTTAAA
1000321 ATTATAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 8 0.36
14 2 0.09
15 12 0.55
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (14 bp):
AGTTTTTTAAATAA
Found at i:1005169 original size:27 final size:27
Alignment explanation
Indices: 1005118--1005170 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1005108 GGCTCAGAAA
*
1005118 CTGACAACTTCTGTGACCCAGTAGCAT
1 CTGACAACTTCTGTGACCCAATAGCAT
*
1005145 CTGATAACTTCTGTG-CCTCAATAGCA
1 CTGACAACTTCTGTGACC-CAATAGCA
1005171 GTTGGTGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.28
Consensus pattern (27 bp):
CTGACAACTTCTGTGACCCAATAGCAT
Found at i:1014716 original size:23 final size:22
Alignment explanation
Indices: 1014688--1014748 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 22
1014678 ATACTGTCTT
*
1014688 TAATATTTCCCTAATAA-AATAA
1 TAATATTTTCCTAA-AATAATAA
*
1014710 TACATATTTTTCTAAAATAATAA
1 TA-ATATTTTCCTAAAATAATAA
1014733 TAATATTTTCCTAAAA
1 TAATATTTTCCTAAAA
1014749 CTAGTTAACC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 17 0.50
23 17 0.50
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (22 bp):
TAATATTTTCCTAAAATAATAA
Found at i:1033689 original size:93 final size:93
Alignment explanation
Indices: 1033530--1033720 Score: 382
Period size: 93 Copynumber: 2.1 Consensus size: 93
1033520 GATCAGGACA
1033530 TCATCTTCAGGAGGGGCATTTGCTTTCTGTTCGCCTTCTTTCTTACATACATCTGCAGCAGTGTA
1 TCATCTTCAGGAGGGGCATTTGCTTTCTGTTCGCCTTCTTTCTTACATACATCTGCAGCAGTGTA
1033595 ACCACCAGAGTTATCCTTTTTCATTACC
66 ACCACCAGAGTTATCCTTTTTCATTACC
1033623 TCATCTTCAGGAGGGGCATTTGCTTTCTGTTCGCCTTCTTTCTTACATACATCTGCAGCAGTGTA
1 TCATCTTCAGGAGGGGCATTTGCTTTCTGTTCGCCTTCTTTCTTACATACATCTGCAGCAGTGTA
1033688 ACCACCAGAGTTATCCTTTTTCATTACC
66 ACCACCAGAGTTATCCTTTTTCATTACC
1033716 TCATC
1 TCATC
1033721 ATCCAACTTT
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 98 1.00
ACGTcount: A:0.19, C:0.27, G:0.16, T:0.38
Consensus pattern (93 bp):
TCATCTTCAGGAGGGGCATTTGCTTTCTGTTCGCCTTCTTTCTTACATACATCTGCAGCAGTGTA
ACCACCAGAGTTATCCTTTTTCATTACC
Done.